Heterogen Section (updated)

The heterogen section of a PDB formatted file contains the complete description of non-standard residues in the entry. Detailed chemical definitions of non-polymer chemical components are described in the Chemical Component Dictionary (https://files.wwpdb.org/pub/pdb/data/monomers)

HET

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 constitute part of a biological polymer and is not one of the following:

standard amino acids, or
standard nucleic acids (C, G, A, U, I, DC, DG, DA, DU, DT and DI), or
unknown amino acid (UNK) or nucleic acid (N) where UNK and N are used to indicate the unknown residue name.

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

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

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 https://files.wwpdb.org/pub/pdb/data/monomers .
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 archive 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, the wwPDB checks that the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records appear, if applicable. The HET record is generated automatically using the Chemical Component 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, there must be corresponding HET, HETNAM, HETSYN, FORMUL,HETATM, and CONECT records. LINK records may also be created.

Example

     1    2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HET  TRS B 975   8
HET  UDP A1457   25                            
HET  B3P A1458   19 
HET  NAG Y  3   15 
HET  FUC Y  4   10 
HET  NON Y  5   12 
HET  UNK A 161    1

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 https://files.wwpdb.org/pub/pdb/data/monomers.
Other names for the group are given on HETSYN records.
PDB entries follow 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 using the Chemical Component Dictionary and information from HETATM records.

Relationships to Other Record Types

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

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETNAM   NAG N-ACETYL-D-GLUCOSAMINE
HETNAM   SAD BETA-METHYLENE SELENAZOLE-4-CARBOXAMIDE ADENINE
HETNAM 2 SAD DINUCLEOTIDE
HETNAM   UDP URIDINE-5'-DIPHOSPHATE 
HETNAM   UNX UNKNOWN ATOM OR ION
HETNAM   UNL UNKNOWN LIGAND 
HETNAM   B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-         
HETNAM  2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

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

The wwPDB does not guarantee 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 be created.

Example

     1     2     3     4     5    6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETSYN   HV5 3-METHYL-L-VALINE 
HETSYN   AB1 ABT-378; LOPINAVIR
HETSYN   CMP CYCLIC AMP; CAMP
HETSYN   TRS TRIS BUFFER;

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 following Hill ordering. The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
The number of each atom type present immediately follows its chemical symbol without an intervening blank space. There will be no number indicated if there is only one atom for a particular atom type.
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. UNL, UNK and UNX will not be listed in FORMUL even though these het groups present in the coordinate section.

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     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
FORMUL 3 MG 2(MG 2+) 
FORMUL 5 SO4 6(O4 S 2-) 
FORMUL 13 HOH *360(H2 O) 
FORMUL 3 NAP 2(C21 H28 N7 O17 P3) 
FORMUL 4 FOL 2(C19 H19 N7 O6) 
FORMUL 5 1PE C10 H22 O6 
FORMUL 2 NX5 C14 H10 O2 CL2 S

Known Problems

Partially deuterated centers are not well represented in this record.