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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