Miscellaneous Features Section

The miscellaneous features section may describe properties in the molecule such as environments surrounding a non-standard residue or the assembly of an active site. Other features may be described in the remarks section but are not given a specific record type so far.


SITE

Overview

  • Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other essential sites or environments surrounding ligands present in the structure.

Record Format

COLUMNS    DATA TYPE  FIELD     DEFINITION
---------------------------------------------------------------------------------
 1 - 6    Record name  "SITE "
 8 - 10    Integer    seqNum    Sequence number.
12 - 14    LString(3)  siteID    Site name.
16 - 17    Integer    numRes    Number of residues that compose the site.
19 - 21    Residue name resName1   Residue name for first residue that 
 creates the site.
23      Character   chainID1   Chain identifier for first residue of site.
24 - 27    Integer    seq1     Residue sequence number for first residue
 of the site.
28      AChar     iCode1    Insertion code for first residue of the site.
30 - 32    Residue name resName2   Residue name for second residue that 
 creates the site.
34      Character   chainID2   Chain identifier for second residue of
 the site.
35 - 38    Integer    seq2     Residue sequence number for second
 residue of the site.
39      AChar     iCode2    Insertion code for second residue
 of the site.
41 - 43    Residue name resName3   Residue name for third residue that 
 creates the site.
45      Character   chainID3   Chain identifier for third residue
 of the site.
46 - 49    Integer    seq3     Residue sequence number for third
 residue of the site.
50      AChar     iCode3    Insertion code for third residue
 of the site.
52 - 54    Residue name resName4   Residue name for fourth residue that 
 creates the site.
56      Character   chainID4   Chain identifier for fourth residue
 of the site.
57 - 60    Integer    seq4     Residue sequence number for fourth
 residue of the site.
61      AChar     iCode4    Insertion code for fourth residue
 of the site.

Details

  • The sequence number (columns 8 - 10) is reset to 1 for each new site.
  • SITE identifiers (columns 12 - 14) should be fully explained in remark 800.
  • If a site is composed of more than four residues, these may be specified on additional records bearing the same site identifier.
  • SITE records can include HET groups.

Verification/Validation/Value Authority Control

Every SITE must have a corresponding description in remark 800. The numbering of sequential SITE records and format of each one is verified, as well as the existence of each residue in the ATOM records.

Relationships to Other Record Types

Each listed SITE needs a corresponding REMARK 800 that details its significance.

Example

 1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SITE   1 AC1 3 HIS A 94 HIS A 96 HIS A 119                
SITE   1 AC2 5 ASN A 62 GLY A 63 HIS A 64 HOH A 328          
SITE   2 AC2 5 HOH A 634                           
SITE   1 AC3 5 GLN A 136 GLN A 137 PRO A 138 GLU A 205          
SITE   2 AC3 5 CYS A 206                           
SITE   1 AC4 11 HIS A 64 HIS A 94 HIS A 96 HIS A 119          
SITE   2 AC4 11 LEU A 198 THR A 199 THR A 200 TRP A 209          
SITE   3 AC4 11 HOH A 572 HOH A 582 HOH A 635      

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