|
|||||
|
Connectivity Annotation SectionThe connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages. SSBONDOverviewThe SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond. 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 oper for 1st resid 67 - 72 SymOP sym2 Symmetry oper for 2nd residDetails
PDB processing programs generate these records automatically Relationships to Other Record TypesCONECT 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 123456789012345678901234567890123456789012345678901234567890123456789012 SSBOND 1 CYS E 48 CYS E 51 2555 SSBOND 2 CYS E 252 CYS E 285 SSBOND 1 CYS A 250 CYS A 277 1555 1555 SSBOND 2 CYS B 250 CYS B 277 1555 1555Known Problems If SG of cysteine is disordered then there are possible alternate linkages. PDB's practice is to put together all possible SSBOND records. This is problematic because the alternate location identifier is not specified in the SSBOND record. LINKOverviewThe LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. 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 for 1st atom. 67 - 72 SymOP sym2 Symmetry operator for 2nd atom.Details
The distance between the pair of atoms listed must be consistent with the bonding. Relationships to Other Record TypesCONECT 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 123456789012345678901234567890123456789012345678901234567890123456789012 LINK O1 DDA 1 C3 DDL 2 LINK MN MN 391 OE2 GLU 217 2565 LINK C LYS A 296 N CME A 297 1555 1555 LINK C CME A 297 N MET A 298 1555 1555 LINK CA CA A 997 O GLN A 262 1555 1555 LINK CA CA A 997 O TRP A 240 1555 1555 LINK CA CA A 997 O HOH Z 169 1555 1555 LINK CA CA A 997 O PRO A 249 1555 1555 CISPEPOverviewCISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides. 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 Measure of the angle in degrees.Details
PDB generates these records automatically. Relationships to Other Record TypesPeptide bonds which deviate significantly from either cis or trans conformation are annotated in REMARK 500. Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 CISPEP 1 GLY A 116 GLY A 117 0 18.50 CISPEP 2 THR D 92 PRO D 93 0 359.80 |