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.

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)