Atomic Coordinate Entry Format Version 3.3
REMARK 300
Description of the biologically functional molecule (biomolecule) in free text. Remark 300 is mandatory if REMARK 350 is provided.
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REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300 FREE TEXT GOES HERE.
Examples
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 DETAILS: THE CATALYTIC SUBUNIT OF LIVER ALCOHOL DEHYDROGENASE FROM REMARK 300 EQUUS CABALLUS IS A HOMODIMER.
Example - Icosahedral virus
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 DETAILS: THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I).
Example - Helical viruses
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 DETAILS: THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -33.23 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 16.00 ANGSTROMS REMARK 300 IN ADDITION, THERE IS 5-FOLD CIRCULAR REMARK 300 SYMMETRY AROUND THE HELIX AXIS
Example - point symmetry crystal structure
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 DETAILS: THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REMARK 300 REGULAR DIHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = D17).
REMARK 350
REMARK 350 presents all transformations, both crystallographic and non-crystallographic, needed to generate the biomolecule. These transformations operate on the coordinates in the entry. Both author and computational descriptions of assemblies are provided, if applicable. For strict ncs case where more than one assembly presents in asymmetric unit, only one chain with unit matrix will reported in REMARK 350, the other chain will be generated by rotation and translation.
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REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I,
REMARK 350 AND CHAINS: J, K, L
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
Note: If entry is part of a SPLIT record (larger multi-protein complex), REMARK 350 represents only the quaternary structure of that split entry.
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 QUATERNARY STRUCTURE FOR THIS ENTRY: 21MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, REMARK 350 AND CHAINS: J, K, L, M, N, O, P, Q, T, REMARK 350 AND CHAINS: S, T, U REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
Example – Author and computed assembly predictions agree
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, REMARK 350 AND CHAINS: J, K, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
Note: The value for the average buried surface area will be round to the nearest 10.
Example – Author and computed assembly predictions differ
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I, J, K, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, REMARK 350 AND CHAINS: J, K, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
Example – When there are no quaternary assemblies provided by either author or software
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
Note that the average buried surface area is not included in this example because the quaternary structure is a monomer.
Example – When software predicts multiple quaternary assemblies
For example, the author states the biological unit to be a dimer, but software predicts the quaternary structure to be either a dimer or a tetramer:
REMARK 300 REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 SURFACE AREA OF THE COMPLEX: 12330 ANGSTROM**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 375
REMARK 375 specifies atoms which lie within 0.15A of a symmetry-related atom and therefore, are considered to be on a special position, with cumulative occupancies of such atoms not exceeding 1.0.
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Example
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 77 LIES ON A SPECIAL POSITION. REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A 13 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 28 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 36 LIES ON A SPECIAL POSITION.
REMARK 400 (updated), Compound
Further details about the macromolecular contents of the entry. The GROUP describes a molecule that is composed of several components which could be polymer sequence and/or het groups.
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REMARK 400
REMARK 400 COMPOUND
REMARK 400 FREE TEXT GOES HERE.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME:
REMARK 400 CHAIN:
REMARK 400 COMPONENT_1:
REMARK 400 COMPONENT_2:
REMARK 400 DESCRIPTION:
Examples
REMARK 400 COMPOUND REMARK 400 THE PRD1 SUS1 MUTANT LACKS THE PACKAGING PROTEIN P9 REMARK 400 AND PRODUCES ONLY EMPTY PARTICLES, WHICH REPRESENT REMARK 400 AN ASSEMBLY INTERMEDIATE REMARK 400 REMARK 400 COMPOUND REMARK 400 COMPONENT OF NAPHTHALENE DIOXYGENASE (NDO) REMARK 400 MULTICOMPONENT ENZYME SYSTEM WHICH CATALYZES THE INCORPORATION REMARK 400 OF BOTH ATOMS OF MOLECULAR OXYGEN INTO NAPHTHALENE TO FORM REMARK 400 CIS-NAPHTHALENE DIHYDRODIOL. REMARK 400 COMPOUND REMARK 400 BALHIMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS REMARK 400 A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS REMARK 400 FURTHER GLYCOSYLATED BY TWO MONOSACCHARIDES: A D-GLUCOSE REMARK 400 AND A 4-OXO-VANCOSAMINE. REMARK 400 HERE, BALHIMYCIN IS REPRESENTED GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND TWO LIGANDS (HET) DVC AND BGC REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BALHIMYCIN REMARK 400 CHAIN: A, B, C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7 REMARK 400 COMPONENT_2: SUGAR RESIDUES 8 AND 9 REMARK 400 DESCRIPTION: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE REMARK 400 GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON REMARK 400 RESIDUE 4 AND BY 4-OXO-VANCOSAMINE REMARK 400 (RESIDUE 9) ON RESIDUE 6.
REMARK 450
Further details about the biological source of the macromolecular contents of the entry.
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1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 450 REMARK 450 SOURCE REMARK 450 FREE TEXT GOES HERE.
REMARK 465, Missing residues
REMARK 465 lists the residues that are present in the SEQRES records but are completely absent from the coordinates section.
Template for non NMR entries
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI
Example
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 46 REMARK 465 GLY A 47 REMARK 465 ALA A 48 REMARK 465 ARG A 49 REMARK 465 MET A 50
Template for NMR entries (new)
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REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS X-YYY
REMARK 465 RES C SSSEQI
The models is listed as a range, X-YYY.
Example
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2
REMARK 470, Missing Atom(s)
Non-hydrogen atoms of standard residues which are missing from the coordinates are listed. Missing HETATMs (atoms) within hetetrogen groups that are in SEQRES are also listed here.
Template for non NMR entries
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS
Example
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 412 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 456 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 486 CG CD OE1 OE2 REMARK 470 GLU A 547 CG CD OE1 OE2 REMARK 470 GLU A 548 CG CD OE1 OE2 REMARK 470 LYS A 606 CG CD CE NZ REMARK 470 ARG B 456 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 484 CG OD1 OD2 REMARK 470 GLN B 485 CG CD OE1 NE2 REMARK 470 GLU B 486 CG CD OE1 OE2 REMARK 470 ARG B 490 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 522 CG CD OE1 OE2 REMARK 470 ARG B 576 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 599 CG OD1 OD2
Template for NMR entries (add)
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS X-YYY REMARK 470 RES CSSEQI ATOMS The models is listed as a range, X-YYY.
Example
REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-25 REMARK 470 RES CSSEQI ATOMS REMARK 470 ILE A 20 CD1 REMARK 470 THR A 59 CG2
REMARK 475, Residues modeled with zero occupancy
REMARK 475 enumerates residues modeled with zero occupancy.
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REMARK 475
REMARK 475 ZERO OCCUPANCY RESIDUES
REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY.
REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT
REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE)
REMARK 475 M RES C SSEQI
Examples
REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 DG D 4 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 24
REMARK 480
REMARK 480 enumerates non-hydrogen atoms in residues modeled with zero occupancy.
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REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
Examples
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 DC D 3 C4' O4' C1' C3' O3' REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 480 I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 26 CG ND1 CD2 CE1 NE2 REMARK 480 HIS B 26 CB CG ND1 CD2 CE1 NE2 REMARK 480 GLU B 52 CD OE1 OE2
REMARK 500, Geometry and Stereochemistry
REMARK 500 provides further details about the stereochemistry of the structure. This REMARK is generated automatically and may incorporate comments provided by the author. It is currently divided into the subtopics:
- CLOSE CONTACTS IN SAME ASYMMETRIC UNIT,
- CLOSE CONTACTS,
- COVALENT BOND LENGTHS,
- COVALENT BOND ANGLES,
- TORSION ANGLES,
- NON-CIS & NON-TRANS,
- PLANAR GROUPS,
- MAIN CHAIN PLANARITY,
- CHIRAL CENTERS.
Additional subtopics may be added as needed. For close contacts, the cutoff limit is 2.2 Angstroms for non-hydrogen atoms and is 1.6 Angstroms for H and D atoms. These distances are listed in the REMARK 500 for close contacts symmetry.
All the calculations on RMSD deviations include all the atoms present in the coordinates including atoms with zero occupancy.
The calculation of bond and angle deviations for protein entries will be based on the updated Engh & Huber amino acid target values1. For nucleic acids, the Parkinson et al., statistics will be used for these calculations2. All bonds and angles that deviate more than 6 times from their standard target values will be flagged as a deviation. The PHI/PSI values are based on the Kleywegt-Jones calculations3.
The improper CA-C-CB-N angles for chiral centers are calculated and are defined below with 10 degree allowed deviations.
+35 for L amino acids
-35 for D amino acids
- +25 to +45 degree range is defined as sp3, L.
If D is expected, it gives "WRONG HAND" in the details. If the calculated value is positive and outside this range, it gives "OUTSIDE RANGE" in the details. - -10 to +10 degree range is defined as sp2, planar.
If it is expected to be sp2 and the value is outside this range, it gives "EXPECTING PLANAR" in the details. If it is expected to be sp3 and the value is within this range, it gives "EXPECTING SP3" in the details. - -45 to -25 degree range is defined as sp3, D.
If L is expected, it gives "WRONG HAND" in the details. If the calculated value is negative and outside this range, it gives "OUTSIDE RANGE" in the details.
The improper CA-C-CB-N angles for chiral centers are calculated for all the alternate conformations. However alt id will not be listed for outliers where residue involves alternate conformations.
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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC:
REMARK 500
REMARK 500 FREE TEXT GOES HERE.
Example – Close Contacts in the same asymmetric unit
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N PHE 1 8 OD2 ASP 1 31 2.17 REMARK 500 OD2 ASP 1 31 N PHE 1 8 2.17 REMARK 500 REMARK 500 THIS ENTRY HAS 104 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL
Example – Close Contacts
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ALA G 153 OD1 ASP H 46 2565 1.84 REMARK 500 CB ALA G 153 OD1 ASP H 46 2565 2.18 REMARK 500 REMARK 500 THIS ENTRY HAS 64 SYMMETRY CONTACTS REMARK 500 REMARK 500 REMARK: NULL
Example – Covalent bond lengths
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN B 117 C ASP B 117 O 0.129 REMARK 500 CYS J 29 CB CYS J 29 SG -0.111 REMARK 500 REMARK 500 REMARK: NULL
Example – Covalent bond angles
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 124 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 PRO B 109 CA - N - CD ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL
Example – Torsion angles
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 100 -110.87 -163.72 REMARK 500 ILE A 166 -28.81 -31.64 REMARK 500 REMARK 500 THIS ENTRY HAS 108 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL
Example – Cis/Trans geometry
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 413 ASP A 414 1 147.84 REMARK 500 ALA B 288 ASN B 289 2 -39.12 REMARK 500 REMARK 500 REMARK: NULL
Example – Planar groups
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 36 0.08 SIDE CHAIN REMARK 500 TYR A 104 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL
Example – Main chain planarity
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 GLY A 289 -10.28 REMARK 500 REMARK 500 REMARK: NULL
Example – Chiral centers
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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER C--N--CA--CB CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 16 LEU A 20 0.1 L D EXPECTING SP3
REMARK 500 16 VAL A 21 -96.0 L D OUTSIDE RANGE
REMARK 500 16 GLN A 22 -54.1 L D OUTSIDE RANGE
REMARK 500 16 THR A 24 -42.0 L D WRONG HAND
REMARK 500 16 LYS A 26 -96.9 L D OUTSIDE RANGE
REMARK 500 16 ARG A 29 -133.0 L D OUTSIDE RANGE
REMARK 500 16 LEU A 31 53.6 L L OUTSIDE RANGE
REMARK 500 16 LYS A 32 -45.4 L D OUTSIDE RANGE
REMARK 500 16 GLU A 33 -41.3 L D WRONG HAND
REMARK 500 16 ASP A 34 -43.2 L D WRONG HAND
REMARK 500
REMARK 500 REMARK: NULL
1Structure quality and target parameters. R. A. Engh and R. Huber. International Tables for Crystallography (2006). Vol. F, ch. 18.3, pp. 382-392
2"New Parameters for the Refinement of Nucleic Acid Containing Structures." G. Parkinson, J. Vojtechovsky, L. Clowney, A. Brunger*, and H. M. Berman. (1996) Acta Cryst. D 52, 57-64
3"PHI/PSI- Chology: Ramachandran revisited. “ G.J. Kleywegt and T.A. Jones (1996) Structure 4, 1395-1400.
REMARK 525, Distant Solvent Atoms
REMARK 525 lists solvent atoms more than 5 Angstroms from any polymer chain.
Template
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 formatted text.
Example
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M=MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 89 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B 94 DISTANCE = 5.58 ANGSTROMS
REMARK 600
Further details on the heterogens in the entry.
Template
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REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 FREE TEXT GOES HERE.
Example
REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 CHAIN A ENDOTHIAPEPSIN: REMARK 600 RESIDUES ASP 54 AND GLY 55 HAVE CYCLISED REMARK 600 TO FORM A SUCCINIMIDE (RESIDUE SUI 54) REMARK 600 REMARK 600 CHAIN B IN THIS PDB ENTRY IS THE REMARK 600 GEM-DIOL INHIBITOR PD-135.040
REMARK 610 and REMARK 615
Ligands or hetgroups that are not part of any polymer (protein or nucleic acid) in the structure may also have missing atoms or atoms with zero occupancy. In such instances the name of the hetgroup or ligand, chain ID and model number (if applicable) will be listed in REMARK 610 (for missing atoms) or REMARK 615 (for atoms with 0.00 occupancy). As the list of specific atoms missing from a hetgroup may be really large, they will not listed in the remarks described above. The list of all missing atoms from the ligands may be easily derived by comparing the coordinates of the hetgroup to its definition in the ligand dictionary.
REMARK 610, Non-polymer residues with missing atoms
REMARK 610 enumerates non-polymer residues with missing atoms.
Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PPI 438
REMARK 615
REMARK 615 enumerates non-polymer residues containing atoms modeled with zero occupancy.
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 PPI 438
REMARK 620
Details of metal coordination are provided in REMARK 620. By default, coordination angles for any metal coordination and surrounding residues (if present) will be provided in this REMARK.
Template:
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 N RES CSSEQI ATOM
Example
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 107 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 F3S A 107 FE3 142.2 REMARK 620 3 F3S A 107 FE4 154.3 59.7 REMARK 620 4 F3S A 107 S1 120.2 53.8 55.7 REMARK 620 5 F3S A 107 S2 113.0 103.5 54.3 106.6 REMARK 620 6 F3S A 107 S3 103.8 53.0 101.7 103.2 109.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 107 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 F3S A 107 FE1 REMARK 620 2 F3S A 107 FE4 59.0 REMARK 620 3 F3S A 107 S1 52.7 55.1 REMARK 620 4 F3S A 107 S3 52.9 101.0 102.1 REMARK 620 5 CYS A 45 SG 146.5 146.2 115.6 112.8 REMARK 620 6 F3S A 107 S4 103.5 54.5 106.3 109.6 110.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 107 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 F3S A 107 FE1 REMARK 620 2 F3S A 107 FE3 61.3 REMARK 620 3 F3S A 107 S1 53.4 53.9 REMARK 620 4 F3S A 107 S2 54.4 105.0 104.5 REMARK 620 5 CYS A 20 SG 142.7 140.2 109.0 114.5 REMARK 620 6 F3S A 107 S4 105.1 54.1 104.8 111.7 111.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 108 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 F3S A 108 S3 REMARK 620 2 CYS A 16 SG 120.1 REMARK 620 3 F3S A 108 FE3 51.4 145.9 REMARK 620 4 F3S A 108 FE4 54.3 148.5 59.9 REMARK 620 5 F3S A 108 S1 98.3 110.0 50.6 101.5 REMARK 620 6 F3S A 108 S2 104.2 109.4 104.5 53.3 114.7 REMARK 620 N 1 2 3 4 5 REMARK 620
REMARK 630 (updated), Inhibitor Description
Details of inhibitor/peptide inhibitor which is presented as a chemical component (het group) are provided in REMARK 630. By default, molecule type and inhibitor’s name will be provided in this REMARK.
Template:
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 630 MOLECULE TYPE: REMARK 630 MOLECULE NAME: REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 SOURCE: REMARK 630 TAXONOMY: REMARK 630 SUBCOMP: REMARK 630 DETAILS:
REMARK 650
Further details on the helical portions of the entry.
Template
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 650 REMARK 650 HELIX REMARK 650 FREE TEXT GOES HERE.
Examples
REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: KDSSP REMARK 650 THE MAJOR DOMAINS ARE: "N" FOR N-TERMINAL DOMAIN, "B" FOR REMARK 650 BETA-BARREL DOMAIN, AND "C" FOR C-TERMINAL DOMAIN. "F" REMARK 650 REFERS TO THE ACTIVE SITE FLAP. ALPHA HELICES ARE NAMED REMARK 650 WITH TWO CHARACTERS, THE FIRST REFERRING TO THE DOMAIN REMARK 650 IN WHICH THEY OCCUR. REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 700, Sheet
Further details on the sheet content of the structure. Several standard templates are shown.
Template
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 700 REMARK 700 SHEET REMARK 700 FREE TEXT GOES HERE.
Examples
REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. STRANDS N1, N2, N3 AND N4 OF SHEET REMARK 700 XXX AND XXX ARE IDENTICAL. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: REMARK 700 THE SHEET PRESENTED AS XXX ON SHEET RECORDS BELOW IS REMARK 700 ACTUALLY AN N-STRANDED BETA-BARREL. THIS IS REMARK 700 REPRESENTED BY A N+1-STRANDED SHEET IN WHICH THE FIRST AND REMARK 700 LAST STRANDS ARE IDENTICAL. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. REMARK 700 EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE REMARK 700 IDENTICAL STRANDS. REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET. REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET.
N1, N2, N3 and N4 represent strand numbers, and XXX represents sheet identifiers.
When the remark for several bifurcated sheets is used, its last line is repeated for the appropriate number of bifurcated sheets, as shown in the last template above.
Examples
REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS are defined. STRANDS 3, 4, AND 5 REMARK 700 OF SHEET *B2A* AND *B2B* ARE IDENTICAL. STRANDS 3, 4, AND REMARK 700 5 OF SHEET *B2C* AND *B2D* ARE IDENTICAL. REMARK 700 REMARK 700 SHEET REMARK 700 STRANDS 1 TO 4 OF THE BETA-SHEET HAVE GREEK-KEY TOPOLOGY. REMARK 700 THE SHEET FORMS A FIVE-STRANDED BETA-BARREL WITH BULGES IN REMARK 700 STRANDS 3 AND 5. IN ORDER TO REPRESENT THIS FEATURE IN THE REMARK 700 SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET PRESENTED AS S5 ON SHEET RECORDS BELOW IS REMARK 700 ACTUALLY A 6-STRANDED BETA-BARREL. THIS IS REMARK 700 REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND REMARK 700 LAST STRANDS ARE IDENTICAL. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800
Further details on important sites of the entry. REMARK 800 is mandatory if SITE records exist.
Template
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REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: FREE TEXT GOES HERE.
REMARK 800 EVIDENCE_CODE: (AUTHOR or SOFTWARE or UNKNOWN)
REMARK 800 SITE_DESCRIPTION: FREE TEXT GOES HERE.
- Site identifiers are 3-letter codes in a character range of AC1-ZZ9 if it is software determined.
Examples
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: RCA REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY REMARK 800 REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY. REMARK 800 REMARK 800 SITE_IDENTIFIER: RCB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY REMARK 800 REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BAT A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BIL A 20
Relationship to other records:
Remark 800 is mandatory if site records exist.
REMARK 900, Related Entries
This REMARK provides information about other PDB entries related to the entry. These may include coordinate entries deposited as a related set, an EMDB identifier for the related EM map, a BMRB identifier for the related NMR chemical shifts, or a structural genomics target identifier.
Template
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REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 FREE TEXT GOES HERE.
Examples
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GB8 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF WT CC-CCP COMPLEX REMARK 900 RELATED ID: 2PCC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WT CC-CCP COMPLEX REMARK 900 RELATED ID: 1YCC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YEAST ISO-1-CYTOCHROME C REMARK 900 RELATED ID: 1ZBY RELATED DB: PDB REMARK 900 HIGH-RESOLUTION CRYSTAL STRUCTURE OF YEAST CYTOCHROME C REMARK 900 PEROXIDASE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: STR82 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15386 RELATED DB: BMRB
REMARK 999, Sequence
This remark is a free text remark which describes anything unusual about a particular polymer sequence in SEQRES records.
For examples,
- If the exact sequence of the sample is not known, due to, for example, proteolysis, the sequence should match the coordinates and a REMARK 999 can be added.
- The information about a sequence region of a chimeric protein which does not match the UNP entry, such as a linker region, can be added to REMARK 999.
- Sequence conflicts which are listed in the UNP reference can also be described in REMARK 999. A full explanation of the microheterogeneity for all residues at a particular residue number can be elaborated in REMARK 999.
- If the coordinates alignment with the sequence is unknown and the residue numbering is arbitrary. The sequence would be poly UNK. The sequence, if it is known, would be listed in the REMARK 999
Template
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 REMARK 999 REMARK 999 SEQUENCE REMARK 999 FREE TEXT GOES HERE.
Example
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE N-TERMINAL 19 RESIDUES 'GSHMVPGQKQHYVQPTAAN' REMARK 999 CORRESPOND TO A PHAGE-DISPLAY DERIVED PEPTIDE, REMARK 999 WHICH IS FUSED TO THE SECRETION CHAPERONE PROTEIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE USED IS THAT PROVIDED BY THE CDNA, WHICH REMARK 999 CORRECTS SEVERAL ASP/ASN AND GLU/GLN MISASSIGNMENTS. REMARK 999 REMARK 999 SEQUENCE REMARK 999 THR AT POSITION 74 WAS FOUND BY WOLMAN ET AL., JOURNAL OF REMARK 999 BIOCHEMISTRY 263, 15506 (1988). REMARK 999 SEQUENCE REMARK 999 THE INSERTED RESIDUES AT THE N-TERMINUS OF THE PROTEIN REMARK 999 CORRESPOND TO A 32-RESIDUE DSE3 LANTHIDE-BINDING TAG REMARK 999 THE RESIDUES NUMBERED 66 TO 100 IN THIS ENTRY CORRESPOND REMARK 999 TO RESIDUES -4 TO 13 AND -1' TO 15' IN THE PRIMARY CITATION.
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