Atomic Coordinate Entry Format Version 3.3
Connectivity Annotation Section
The connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages.
SSBOND
The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.
The disulfide bond distance is included after the symmetry operations at the end of the SSBOND record.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------------------------------- 1 - 6 Record name "SSBOND" 8 - 10 Integer serNum Serial number. 12 - 14 LString(3) "CYS" Residue name. 16 Character chainID1 Chain identifier. 18 - 21 Integer seqNum1 Residue sequence number. 22 AChar icode1 Insertion code. 26 - 28 LString(3) "CYS" Residue name. 30 Character chainID2 Chain identifier. 32 - 35 Integer seqNum2 Residue sequence number. 36 AChar icode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator for residue 1. 67 - 72 SymOP sym2 Symmetry operator for residue 2. 74 – 78 Real(5.2) Length Disulfide bond distance
Details
- Bond distances between the sulfur atoms must be close to expected value.
- sym1 and sym2 are right justified and are always given even when identity operator (no cell translation) is to be applied to the residue.
Verification/Validation/Value Authority Control
wwPDB processing programs generate these records automatically.
Relationships to Other Record Types
CONECT records are generated for the disulfide bonds when SG atoms of both cysteines are present in the coordinate records.
Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.07 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.06 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04
Known Problems
If SG of cysteine is disordered then there are possible alternate linkages. wwPDB practice is to put together all possible SSBOND records. This is problematic because the alternate location identifier is not specified in the SSBOND record.
LINK
Overview
The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. They also include the distance associated with the each linkage following the symmetry operations at the end of each record.
This record supplements information given in CONECT records and is provided here for convenience in searching.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------------ 1 - 6 Record name "LINK " 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1 Residue name. 22 Character chainID1 Chain identifier. 23 - 26 Integer resSeq1 Residue sequence number. 27 AChar iCode1 Insertion code. 43 - 46 Atom name2 Atom name. 47 Character altLoc2 Alternate location indicator. 48 - 50 Residue name resName2 Residue name. 52 Character chainID2 Chain identifier. 53 - 56 Integer resSeq2 Residue sequence number. 57 AChar iCode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator atom 1. 67 - 72 SymOP sym2 Symmetry operator atom 2. 74 – 78 Real(5.2) Length Link distance
Details
- The atoms involved in bonds between HET groups or between a HET group and standard residue are listed.
- Inter-residue linkages not implied by the primary structure are listed (e.g., reduced peptide bond).
- Non-standard linkages between residues, e.g., side-chain to side-chain, are listed.
- Each LINK record specifies one linkage.
- These records do not specify connectivity within a HET group (see CONECT) or disulfide bridges (see SSBOND).
- sym1 and sym2 are right justified and are given as blank when the identity operator (and no cell translation) is to be applied to the atom.
- For NMR entries, only one set (or model) of LINK records will be supplied. - Coordinate bonds are also listed as LINKs
Verification/Validation/Value Authority Control
The distance between the pair of atoms listed must be consistent with the bonding.
Relationships to Other Record Types
CONECT records are generated from LINKs when both atoms are present in the entry. If symmetry operators are given to generate one of the residues involved in the bond, REMARK 290 defines the symmetry transformation.
Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 LINK O GLY A 49 NA NA A6001 1555 1555 2.98 LINK OG1 THR A 51 NA NA A6001 1555 1555 2.72 LINK OD2 ASP A 66 NA NA A6001 1555 1555 2.72 LINK NE ARG A 68 NA NA A6001 1555 1555 2.93 LINK NE ARG A 68 NA NA A6001 1555 1555 2.93 LINK C21 2EG A 7 C22 2EG B 19 1555 1555 1.56
CISPEP
Overview
CISPEP records specify the prolines and other peptides found to be in the cis conformation. Each cis peptide is listed on a separate line, with a consecutive numbering sequence.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------- 1 - 6 Record name "CISPEP" 8 - 10 Integer serNum Record serial number. 12 - 14 LString(3) pep1 Residue name. 16 Character chainID1 Chain identifier. 18 - 21 Integer seqNum1 Residue sequence number. 22 AChar icode1 Insertion code. 26 - 28 LString(3) pep2 Residue name. 30 Character chainID2 Chain identifier. 32 - 35 Integer seqNum2 Residue sequence number. 36 AChar icode2 Insertion code. 44 - 46 Integer modNum Identifies the specific model. 54 - 59 Real(6.2) measure Angle measurement in degrees.
Details
- Cis peptides are those with omega angles of 0°±30°. Deviations larger than 30° are listed in REMARK 500.
Verification/Validation/Value Authority Control
These records are generated automatically.
Relationships to Other Record Types
Peptide bonds which deviate significantly from either the cis or trans conformation are annotated in REMARK 500.
Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
CISPEP 1 SER A 58 GLY A 59 0 20.91
CISPEP 1 GLY A 116 GLY A 117 0 18.50
CISPEP 1 MET A 1 SER A 2 0 -3.69