About
PDBms is an online tool for PDB file splitting and interactive 3D molecular visualization of molecules. It parses coordinate section records in the PDB file and categorizes them into a group of molecules. Moreover, it supports 3D visualization of various protein-ligand interactions and different models. The customized PDB file consists of Title (HEADER, TITLE), Primary Structure (SEQRES), Heterogen (HETNAM, FORMUL), Coordinate (ATOM, ANISOU, TER, HETATM), and Connectivity (CONECT) records. A brief description of PDB records are below,
PDB Records
A standard PDB file has represented in lines (rows) that consist of 80 columns. Each line has a record name that starts with a unique keyword (in the first six columns). The last character in each PDB entry has an end-of-line (EOL) indicator. Each record type consists of multiple lines and fields separated by spaces. A broad category of sections and a short description of each record are below.
| Sections | Records | Description |
|---|---|---|
| Title | HEADER, OBSLTE, TITLE, SPLIT, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK | It consists of records that describe the experiment and the biological macromolecules. |
| Primary Structure | DBREF, DBREF1 / DBREF2, SEQADV, SEQRES, and MODRES | It consists of the sequence of chains in the macromolecule and references to the database. |
| Heterogen | HET, FORMUL, HETNAM, and HETSYN | It consists of the description of non-standard residues (heteroatoms). |
| Secondary Structure | HELIX, and SHEET | It contains the secondary structure (helices and sheets) of protein and polypeptides. |
| Connectivity Annotation | SSBOND, LINK, and CISPEP | It contains the description of the existence and location of disulfide bonds and other linkages. |
| Miscellaneous Features | SITE | It describes the properties in the molecule, such as environments surrounding a heteroatom or the assembly of an active site. |
| Crystallographic and Coordinate Transformation | CRYST1, MTRIXn, ORIGXn, and SCALEn | It describes the geometry of the crystallographic experiment and the coordinate system transformations. |
| Coordinate | MODEL, ATOM, ANISOU, TER, HETATM, and ENDMDL | It contains the atomic coordinates of the molecules. |
| Connectivity | CONECT | It consists of details of atom connections. |
| Bookkeeping | MASTER, and END | It describes the file itself. |
Title Section
This section consists of records that describe the experiment and the biological macromolecules.
HEADER Record
The HEADER record provides a summary of the molecules.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | HEADER | Header record identifier |
| 11 - 50 | String(40) | classification | Classifies the molecule(s). It may be based on function, metabolic role, molecule type, cellular location, etc. |
| 51 - 59 | Date | depDate | Deposition date. This is the date the coordinates were received at the PDB. |
| 63 - 66 | IDcode | idCode | This identifier is unique within the PDB. |
TITLE Record
The TITLE record consists of a title for the experiment or analysis of the molecule.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | TITLE | Title record identifier |
| 9 - 10 | continuation | continuation | Allows concatenation of multiple records. |
| 11 - 80 | String | title | Title of the experiment. |
Primary Structure Section
The primary structure section consists of the sequence of chains in the macromolecule and references to the database.
SEQRES Record
The SEQRES records contain the sequence of chains in the macromolecule represented by triple-letters.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | SEQRES | Seqres record identifier |
| 8 - 10 | Integer | serNum | Serial number of the SEQRES record for the current chain. Starts at 1 and increments by one each line. Reset to 1 for each chain. |
| 12 | Character | chainID | Chain identifier. This may be any single legal character, including a blank which is is used if there is only one chain. |
| 14 - 17 | Integer | numRes | Number of residues in the chain. This value is repeated on every record. |
| 20 - 22 | Residue name | resName | Residue name. |
| 24 - 26 | Residue name | resName | Residue name. |
| 28 - 30 | Residue name | resName | Residue name. |
| 32 - 34 | Residue name | resName | Residue name. |
| 36 - 38 | Residue name | resName | Residue name. |
| 40 - 42 | Residue name | resName | Residue name. |
| 44 - 46 | Residue name | resName | Residue name. |
| 48 - 50 | Residue name | resName | Residue name. |
| 52 - 54 | Residue name | resName | Residue name. |
| 56 - 58 | Residue name | resName | Residue name. |
| 60 - 62 | Residue name | resName | Residue name. |
| 64 - 66 | Residue name | resName | Residue name. |
| 68 - 70 | Residue name | resName | Residue name. |
Heterogen Section
The heterogen section consists of the description of non-standard residues (heteroatoms).
HETNAM Record
This HETNAM record consists of the chemical name of the heteroatoms.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | HETNAM | Hetnam record identifier |
| 9 - 10 | Continuation | continuation | Allows concatenation of multiple records. |
| 12 - 14 | LString(3) | hetID | Het identifier, right-justified. |
| 16 - 70 | String | text | Chemical name. |
FORMUL Record
The FORMUL record consists of the chemical formula and charge of the heteroatoms.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | FORMUL | Formul record identifier |
| 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. |
Coordinate Section
The Coordinate Section contains the atomic coordinates of the molecules.
ATOM/HETATM Record
The ATOM record consists of atomic coordinates, occupancy, and temperature factor of polymers (amino acids and nucleotides). Correspondingly HETATM records for non-polymers.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | ATOM or HETATM | Atom record identifier |
| 7 - 11 | Integer | serial | Atom serial number. |
| 13 - 16 | Atom | name | Atom name. |
| 17 | Character | altLoc | Alternate location indicator. |
| 18 - 20 | Residue name | resName | Residue name. |
| 22 | Character | chainID | Chain identifier. |
| 23 - 26 | Integer | resSeq | Residue sequence number. |
| 27 | AChar | iCode | Code for insertion of residues. |
| 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. |
| 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. |
| 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. |
| 55 - 60 | Real(6.2) | occupancy | Occupancy. |
| 61 - 66 | Real(6.2) | tempFactor | Temperature factor. |
| 73 - 76 | LString(4) | segID | Segment identifier, left-justified. |
| 77 - 78 | LString(2) | element | Element symbol, right-justified. |
| 79 - 80 | LString(2) | charge | Charge of the atom. |
ANISOU Records
The ANISOU consists of anisotropic temperature factors.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | ANISOU | Atom record identifier |
| 7 - 11 | Integer | serial | Atom serial number. |
| 13 - 16 | Atom | name | Atom name. |
| 17 | Character | altLoc | Alternate location indicator. |
| 18 - 20 | Residue name | resName | Residue name. |
| 22 | Character | chainID | Chain identifier. |
| 23 - 26 | Integer | resSeq | Residue sequence number. |
| 27 | AChar | iCode | Insertion code. |
| 29 - 35 | Integer | u[0][0] | U(1,1) |
| 36 - 42 | Integer | u[1][1] | U(2,2) |
| 43 - 49 | Integer | u[2][2] | U(3,3) |
| 50 - 56 | Integer | u[0][1] | U(1,2) |
| 57 - 63 | Integer | u[0][2] | U(1,3) |
| 64 - 70 | Integer | u[1][2] | U(2,3) |
| 73 - 76 | LString(4) | segID | Segment identifier, left-justified. |
| 77 - 78 | LString(2) | element | Element symbol, right-justified. |
| 79 - 80 | LString(2) | charge | Charge on the atom. |
TER Record
The TER record indicates the end of a chain in the ATOM/HETATM records.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | TER | Ter record identifier |
| 7 - 11 | Integer | serial | Atom serial number. |
| 18 - 20 | Residue name | resName | Residue name. |
| 22 | Character | chainID | Chain identifier. |
| 23 - 26 | Integer | resSeq | Residue sequence number. |
| 27 | AChar | iCode | Insertion code. |
Connectivity Section
The connectivity section consists of details of atom connections.
CONECT Record
The CONECT records contain details of atom connections of polymers and heteroatoms.
| Columns | Data Type | Field | Definition |
|---|---|---|---|
| 1 - 6 | Record name | CONECT | Conect record identifier |
| 7 - 11 | Integer | serial | Atom serial number. |
| 12 - 16 | Integer | serial | Serial number of bonded atom |
| 17 - 21 | Integer | serial | Serial number of bonded atom |
| 22 - 26 | Integer | serial | Serial number of bonded atom |
| 27 - 31 | Integer | serial | Serial number of bonded atom |
Reference
Atomic Coordinate Entry Format Version 3.3 - https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html (Updated on 2021-03-01)