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 (ftp://ftp.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 ftp://ftp.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    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 ftp://ftp.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.