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PDB FORMAT Version 2.3
Main Index
HET
HETNAM
HETSYN
FORMUL

Heterogen Section

The heterogen section of a PDB file contains the complete description of non-standard residues in the entry.

HET

Overview

HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are not part of a biological polymer described in SEQRES and considered to be a molecule bound to the polymer, or they are a chemical species that constitutes part of a biological polymer that is not one of the following:

  • not one of the standard amino acids, and
  • not one of the nucleic acids (C, G, A, T, U, and I), and
  • not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.

    • Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNL (Unknown Ligand).

    Record Format 

    COLUMNS DATA TYPE FIELD DEFINITION
------------------------------------------------------
 1 - 6 Record name "HET "
 8 - 10 LString(3) hetID Het identifier, right-justified.
13 Character ChainID Chain identifier.
14 - 17 Integer seqNum Sequence number.
18 AChar iCode Insertion code.
21 - 25 Integer numHetAtoms Number of HETATM records for the
 group present in the entry.
31 - 70 String text Text describing Het group.

    Details

  • Each HET group is assigned a hetID of not more than three (3) alphanumeric characters. The sequence number, chain identifier, insertion code, and number of coordinate records are given for each occurrence of the HET group in the entry. The chemical name of the HET group is given in the HETNAM record and synonyms for the chemical name are given in the HETSYN records, see http://deposit.pdb.org/public-component-erf.cif.
  • There is a separate HET record for each occurrence of the HET group in an entry.
  • A particular HET group is represented in the PDB archives with a unique hetID.
  • PDB entries do not have HET records for water molecules, deuterated water, or methanol (when used as solvent).
  • Unknown atoms or ions will be represented as UNX with the chemical formula X1. Unknown ligands are UNL; unknown amino acids are UNK.

    • Verification/Validation/Value Authority Control

    For each het group that appears in the entry, PDB checks that the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records appear, if applicable. The HET record is generated automatically by PDB using the het group dictionary and information from the HETATM records.

    Each unique hetID represents a unique molecule.

    Relationships to Other Record Types

    For each het group that appears in the entry, the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records must appear, if applicable. LINK records may also appear.

    Example 

     1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
HET TRS 975 8
HET STA I 4 25 PART_OF: HIV INHIBITOR;
HET FUC Y 1 10 PART_OF: NONOATE COMPLEX; L-FUCOSE 
HET GAL Y 2 11 PART_OF: NONOATE COMPLEX 
HET NAG Y 3 15 
HET FUC Y 4 10 
HET NON Y 5 12 
HET UNX A 161 1 PSEUDO CARBON ATOM OF UNKNOWN LIGAND
HET UNX A 162 1 PSEUDO CARBON ATOM OF UNKNOWN LIGAND
HET UNX A 163 1 PSEUDO CARBON ATOM OF UNKNOWN LIGAND

    HETNAM

    Overview

    This record gives the chemical name of the compound with the given hetID.

    Record Format 

    COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------
 1 - 6 Record name "HETNAM"
 9 - 10 Continuation continuation Allows concatenation of
 multiple records.
12 - 14 LString(3) hetID Het identifier,
 right-justified.
16 - 70 String text Chemical name.

    Details

  • Each hetID is assigned a unique chemical name for the HETNAM record, see http://deposit.pdb.org/public-component-erf.cif.
  • Other names for the group are given on HETSYN records.
  • PDB follows IUPAC/IUB naming conventions to describe groups systematically.
  • The special character "~" is used to indicate superscript in a heterogen name. For example: N6 will be listed in the HETNAM section as N~6~, with the ~ character indicating both the start and end of the superscript in the name, e.g.,

    • N-(BENZYLSULFONYL)SERYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLYCINAMIDE

  • Continuation of chemical names onto subsequent records is allowed.
  • Only one HETNAM record is included for a given hetID, even if the same hetID appears on more than one HET record.

    • Verification/Validation/Value Authority Control

    For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM and CONECT records must appear. The HETNAM record is generated automatically by PDB using the het group dictionary and information from HETATM records.

    Relationships to Other Record Types

    For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. HETSYN and LINK records may also appear.

    Example 

     1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
HETNAM GLC GLUCOSE
HETNAM SAD BETA-METHYLENE SELENAZOLE-4-CARBOXAMIDE ADENINE
HETNAM 2 SAD DINUCLEOTIDE
HETNAM UNX UNKNOWN ATOM OR ION
HETNAM UNL UNKNOWN LIGAND 
HETNAM CYE 45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15, 
HETNAM 2 CYE 20,26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37, 
HETNAM 3 CYE 42,45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4, 
HETNAM 4 CYE 7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA- 
HETNAM 5 CYE 1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35, 
HETNAM 6 CYE 44(47)-DODECAENE

    HETSYN

    Overview

    This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetID) HETNAM record. This is to allow greater flexibility in searching for HET groups.

    Record Format 

    COLUMNS DATA TYPE FIELD DEFINITION
--------------------------------------------------------
 1 - 6 Record name "HETSYN"
 9 - 10 Continuation continuation Allows concatenation of
 multiple records.
12 - 14 LString(3) hetID Het identifier,
 right-justified.
16 - 70 SList hetSynonyms List of synonyms.

    Details

  • This is not guaranteed to be a complete list of possible synonyms. New synonyms may be added. The list can be continued onto additional HETSYN records. Even if the same hetID appears on more than one HET record, only one set of HETSYN records is included for the hetID.

    • Verification/Validation/Value Authority Control

    For each HETSYN record in the entry, the corresponding HET, HETNAM, FORMUL, HETATM and CONECT records must appear.

    Relationships to Other Record Types

    If there is a HETSYN record there must be corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records. LINK records may also appear.

    Example 

     1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
HETSYN NAD NICOTINAMIDE ADENINE DINUCLEOTIDE
HETSYN COA COA
HETSYN CMP CYCLIC AMP; CYCLIC ADENOSINE MONOPHOSPHATE
HETSYN TRS TRIS BUFFER; TRISAMINE; 
HETSYN 2 TRS TRIS(HYDROXYMETHYL)AMINOMETHANE; TRIMETHYLOL
HETSYN 3 TRS AMINOMETHANE

    FORMUL

    Overview

    The FORMUL record presents the chemical formula and charge of a non-standard group.

    Record Format 

    COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------
 1 - 6 Record name "FORMUL"
 9 - 10 Integer compNum Component number.
13 - 15 LString(3) hetID Het identifier.
17 - 18 Integer continuation Continuation number.
19 Character asterisk "*" for water.
20 - 70 String text Chemical formula.

    Details

  • The elements of the chemical formula are given in the order C, H, N, and O, with other elements following in alphabetical order, each separated by a single blank.
  • The number of each atom type present immediately follows its chemical symbol with no intervening blank.
  • Each set of SEQRES records and each HET group is assigned a component number in an entry. These numbers are assigned serially, beginning with 1 for the first set of SEQRES records. In addition: 

    • - If a HET group is presented on a SEQRES record its FORMUL is 
 assigned the component number of the chain in which it appears.
- If the HET group occurs more than once and is not presented on 
 SEQRES records, the component number of its first occurrence is used.

  • All occurrences of the HET group within a chain are grouped together with a multiplier. The remaining occurrences are also grouped with a multiplier. The sum of the multipliers is the number equaling the number of times that that HET group appears in the entry.
  • A continuation field is provided in the event that more space is needed for the formula. Columns 17 - 18 are used in order to maintain continuity with the existing format.

    • Verification/Validation/Value Authority Control

    For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. The FORMUL record is generated automatically by PDB processing programs using the het group template file and information from HETATM records.

    Relationships to Other Record Types

    For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear.

    Example 

     1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
FORMUL 2 SO4 2(O4 S1 2-)
FORMUL 3 GLC C6 H12 O6
FORMUL 3 FOL 2(C19 H17 N7 O6 2-)
FORMUL 4 CL 2(CL1 1-) 
FORMUL 5 CA CA1 2+ 
FORMUL 1 ACE C2 H3 O1 
FORMUL 2 ACE C2 H3 O1
FORMUL 8 HOH *463(H2 O1)

    Known Problems

    Partially deuterated centers are not well represented in this record.

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