Overview
The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
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1 - 6 Record name "MODRES"
8 - 11 IDcode idCode ID code of this entry.
13 - 15 Residue name resName Residue name used in this entry.
17 Character chainID Chain identifier.
19 - 22 Integer seqNum Sequence number.
23 AChar iCode Insertion code.
25 - 27 Residue name stdRes Standard residue name.
30 - 70 String comment Description of the residue
modification.
Details
* Residues modified post-translationally, enzymatically, or by design are described in MODRES records. In those cases where PDB has opted to use a non-standard residue name for the residue, MODRES also provides a mapping to the precursor standard residue name.
* MODRES is mandatory for when modified standard residues exist in the entry.
* Examples of some modification descriptions:
Glycosylation site
Post-translational modification
Designed chemical modification
Phosphorylation site
Blocked N-terminus
Aminated C-terminus
D-configuration
Reduced peptide bond
* MODRES is not required if coordinate records are not provided for the modified residue.
* D-amino acids are given their own resName , i.e., DAL for D-alanine. This resName appears in the SEQRES records, and has the associated SEQADV, MODRES, HET, and FORMUL records. The coordinates are given as HETATMs within the ATOM records and occur in the correct order within the chain. This ordering is an exception to the stated Order of Records.
* When a standard residue name is used to describe a modified site, resName (columns 13-15) and stdRES (columns 25-27) contain the same value.
Verification/Validation/Value Authority Control
MODRES is generated by the PDB.
Relationships to Other Record Types
MODRES maps ATOM and HETATM records to the standard residue names. SEQADV, HET, and FORMUL may also appear.
Example
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
MODRES 1ABC ASN A 22A ASN GLYCOSYLATION SITE
MODRES 2ABC TTQ A 50A TRP POST-TRANSLATIONAL MODIFICATION
MODRES 3ABC DAL A 32 ALA POST-TRANSLATIONAL MODIFICATION,D-ALANINE
MODRES 3ABC DAL B 32 ALA POST-TRANSLATIONAL MODIFICATION,D-ALANINE
Known Problems
Mapping between SEQRES and MODRES residue numbers when the numbering is non-sequential has to be constructed using DBREF, SEQRES, and SEQADV.