PDB FORMAT Version 2.3

Connectivity Annotation Section

The connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages.

SSBOND

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 oper for 1st resid
67 - 72 SymOP sym2 Symmetry oper for 2nd resid

Details

Bond distances between the sulfur atoms must be close to expected values.

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

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 
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 1555

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.

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. 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 atoms involved in bonds between HET groups or between a HET group and standard residue are listed.

Interresidue 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 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.

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
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

CISPEP

Overview

CISPEP 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

Cis peptides are those with omega angles of 0��30�. Deviations larger than 30� are listed in REMARK 500.

Each cis peptide is listed on a separate line, with an incrementally ascending sequence number.

Verification/Validation/Value Authority Control

PDB generates these records automatically.

Relationships to Other Record Types

Peptide 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

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