The connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages.
Overview
The 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 operator for 1st residue. 67 - 72 SymOP sym2 Symmetry operator for 2nd residue.
Details
* Bond distances between the sulfur atoms must be close to expected values.
* The cysteine closer to the N-terminal is listed first in each intra-chain pair. The cysteine which occurs first in the coordinate entry is listed first for inter-chain pairs.
* sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the residue.
Verification/Validation/Value Authority Control
PDB processing programs generate these records automatically. If the depositor supplies these records, they are compared to those generated and the depositor is notified of any differences.
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. If symmetry operators are given to generate one of the residues involved in the disulfide bond, REMARK290 defines the symmetry transformation.
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
Known 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.