Introduction

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, bibliographic citations, primary and secondary structure, information, and crystallographic structure factors and NMR experimental data.

This guide describes the "PDB format" used by the members of the worldwide Protein Data Bank (Berman, H.M., Henrick, K. and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol, 10, 980). Questions should be sent to info@wwpdb.org

This version of the PDB file format has been in use since July 9, 1998. Please note that as of July 1, 2002, models are available from a directory separate from the main archive at FTP Site. As of October 15, 2006, theoretical models are no longer accepted for deposition.

Basic Notions of the Format Description

Only non-control ASCII characters, as well as the space and end-of-line indicator, appear in a PDB coordinate entry file. Namely:

abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
1234567890
` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : " < > ?

We discourage use of punctuation characters in the place of alphanumeric characters.

The space, and end-of-line:. The end-of-line indicator is system-specific. Unix uses a line feed character; other systems may use a carriage return followed by a line feed.

Greek letters are spelled out, i.e., alpha, beta, gamma, etc.

Bullets are represented as (DOT).

Right arrow is represented as -->.

Left arrow is represented as <--.

If "=" is surrounded by at least one space on each side, then it is assumed to be an equal sign, e.g., 2 + 4 = 6.

Commas, colons, and semi-colons are used as list delimiters in records that have one of the following data types:

If a comma, colon, or semi-colon is used in any context other than as a delimiting character, then the character must be escaped, i.e., immediately preceded by a backslash, "\". Examples of this use are found in line 4 of each of the following:

COMPND        MOL_ID: 1;
COMPND      2 MOLECULE: GLUTATHIONE SYNTHETASE;
COMPND      3 CHAIN: A;
COMPND      4 SYNONYM: GAMMA-L-GLUTAMYL-L-CYSTEINE\:GLYCINE LIGASE
COMPND      5 (ADP-FORMING);
COMPND      6 EC: 6.3.2.3;
COMPND      7 ENGINEERED: YES

COMPND        MOL_ID: 1;
COMPND      2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHETASE;
COMPND      3 CHAIN: A, B;
COMPND      4 SYNONYM: MAT, ATP\:L-METHIONINE S-ADENOSYLTRANSFERASE;
COMPND      5 EC: 2.5.1.6;
COMPND      6 ENGINEERED: YES;
COMPND      7 BIOLOGICAL_UNIT: TETRAMER;
COMPND      8 OTHER_DETAILS: TETRAGONAL MODIFICATION

Record Format

Every PDB file may be broken into a number of lines terminated by an end-of-line indicator. Each line in the PDB entry file consists of 80 columns. The last character in each PDB entry should be an end- of- line indicator.

Each line in the PDB file is self-identifying. The first six columns of every line contain a record name, left-justified and blank-filled. This must be an exact match to one of the stated record names.

The PDB file may also be viewed as a collection of record types. Each record type consists of one or more lines.

Each record type is further divided into fields.

Each record type is detailed in this document. The description of each record type includes the following sections:

For records that are fully described in fixed column format, columns not assigned to fields must be left blank.

Types of Records

It is possible to group records into categories based upon how often the record type appears in an entry.

Single: There are records that may only appear one time (without continuations) in a file. Listed alphabetically, these are:

RECORD TYPE      DESCRIPTION
--------------------------------------------------------------------
CRYST1           Unit cell parameters, space group, and Z.
END              Last record in the file.
HEADER           First line of the entry, contains PDB ID code,
                 classification, and date of deposition.
MASTER           Control record for bookkeeping.
ORIGXn           Transformation from orthogonal coordinates to the
                 submitted coordinates (n = 1, 2, or 3).
SCALEn           Transformation from orthogonal coordinates to fractional
                 crystallographic coordinates (n = 1, 2, or 3).

It is an error for a duplicate of any of these records to appear in an entry.

There are records that conceptually exist only once in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE      DESCRIPTION
---------------------------------------------------------------------
AUTHOR           List of contributors.
CAVEAT           Severe error indicator
COMPND           Description of macromolecular contents of the entry.
EXPDTA           Experimental technique used for the structure
                 determination.
KEYWDS           List of keywords describing the macromolecule.
OBSLTE           Statement that the entry has been removed from
                 Distribution and list of the ID code(s) which
                 replaced it.
SOURCE           Biological source of macromolecules in the entry.
SPRSDE           List of entries withdrawn from release and replaced by
                 current entry.
TITLE            Description of the experiment represented in the entry.

The second and subsequent lines contain a continuation field, which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Multiple: Most record types appear multiple times, often in groups where the information is not logically concatenated but is presented in the form of a list. Many of these record types have a custom serialization that may be used not only to order the records, but also to connect to other record types. Listed alphabetically, these are:

RECORD TYPE      DESCRIPTION
-----------------------------------------------------------------------
ANISOU           Anisotropic temperature factors.
ATOM             Atomic coordinate records for standard groups.
CISPEP           Identification of peptide residues in cis conformation.
CONECT           Connectivity records.
DBREF            Reference to the entry in the sequence database(s).
HELIX            Identification of helical substructures.
HET              Identification of non-standard groups or residues
                 (heterogens)
HETSYN           Synonymous compound names for heterogens.
LINK             Identification of inter-residue bonds.
MODRES           Identification of modifications to standard residues.
MTRIXn           Transformations expressing non-crystallographic symmetry
                 (n = 1, 2, or 3). There may be multiple sets of these
	            records.
REVDAT           Revision date and related information.
SEQADV           Identification of conflicts between PDB and the named
                 Sequence database.
SEQRES           Primary sequence of backbone residues.
SHEET            Identification of sheet substructures.
SIGATM           Standard deviations of atomic parameters.
SIGUIJ           Standard deviations of anisotropic temperature factors.
SITE             Identification of groups comprising important sites.
SSBOND           Identification of disulfide bonds.
TVECT            Translation vector for infinite covalently connected
                 structures.

There are records that conceptually exist multiple times in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE     DESCRIPTION
---------------------------------------------------------------------
FORMUL          Chemical formula of non-standard groups.
HETATM          Atomic coordinate records for heterogens.
HETNAM          Compound name of the heterogens.

The second and subsequent lines contain a continuation field which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Grouping: There are three record types used to group other records. Listed alphabetically, these are:

RECORD TYPE    DESCRIPTION
---------------------------------------------------------------------
ENDMDL         End-of-model record for multiple structures in a single
               coordinate entry.
MODEL          Specification of model number for multiple structures in a
               single coordinate entry.
TER            Chain terminator.

The MODEL/ENDMDL records surround groups of ATOM, HETATM, SIGATM, ANISOU, SIGUIJ, and TER records. TER records indicate the end of a chain.

Other: The remaining record types have a detailed inner structure. Listed alphabetically, these are:

RECORD TYPE DESCRIPTION -------------------------------------------------------------------- JRNL Literature citation that defines the coordinate set. REMARK General remarks, some are structured and some are free form.

PDB Format Change Policy

The PDB will use the following protocol in making changes to the way PDB coordinate entries are represented and archived. The purpose of the new policy is to allow ample time for everyone to understand these changes and to assess their impact on existing programs. These modifications are necessary to address the changing needs of our users as well as the changing nature of the data that is archived.

Order of Records

All records in a PDB coordinate entry must appear in a defined order. Mandatory record types are present in all entries. When mandatory data are not provided, the record name must appear in the entry with a NULL indicator. Optional items become mandatory when certain conditions exist. Record order and existence are described in the following table:

RECORD TYPE            EXISTENCE   CONDITIONS IF OPTIONAL
--------------------------------------------------------------
HEADER                 Mandatory
OBSLTE                 Optional    Mandatory in withdrawn entries.
TITLE                  Mandatory
CAVEAT                 Optional    Typically included if there are chirality errors
COMPND                 Mandatory
SOURCE                 Mandatory
KEYWDS                 Mandatory
EXPDTA                 Mandatory
AUTHOR                 Mandatory
REVDAT                 Mandatory
SPRSDE                 Optional    Mandatory if a replacement entry.
JRNL                   Optional    Mandatory if a publication Describes the experiment.
REMARK 1               Optional
REMARK 2               Mandatory
REMARK 3               Mandatory
REMARK N               Optional    Mandatory under certain conditions, as noted in the
                                   remark descriptions.
DBREF                  Optional    Mandatory for each peptide chain with a length greater
                                   than ten (10) residues, and for nucleic acid entries
                                   that exist in the NDB.
SEQADV                 Optional    Mandatory if sequence conflict exists.
SEQRES                 Optional    Mandatory if ATOM records exist.
MODRES                 Optional    Mandatory if modified group exists
                                   within the coordinates.
HET                    Optional    Mandatory if non-standard group other
                                   than water appears in the entry.
HETNAM                 Optional    Mandatory if non-standard group other
                                   than water appears in the entry.
HETSYN                 Optional
FORMUL                 Optional    Mandatory if non-standard group or water appears.
HELIX                  Optional
SHEET                  Optional
TURN                   Optional    Deprecated.
SSBOND                 Optional    Mandatory if disulfide bond is present.
LINK                   Optional
HYDBND                 Optional    Deprecated.
SLTBRG                 Optional    Deprecated.
CISPEP                 Optional
SITE                   Optional
CRYST1                 Mandatory
ORIGX1 ORIGX2 ORIGX3   Mandatory
SCALE1 SCALE2 SCALE3   Mandatory
MTRIX1 MTRIX2 MTRIX3   Optional    Mandatory if the complete asymmetric
                                   unit must be generated from the given
                                   coordinates using non-crystallographic symmetry.
TVECT                   Optional
MODEL                   Optional   Mandatory if more than one model
                                   is present in the entry.
ATOM                    Optional   Mandatory if standard residues exist.
SIGATM                  Optional
ANISOU                  Optional
SIGUIJ                  Optional
TER                     Optional   Mandatory if ATOM records exist.
HETATM                  Optional   Mandatory if non-standard group
                                   appears.
ENDMDL                  Optional   Mandatory if MODEL appears.
CONECT                  Optional   Mandatory if non-standard group
                                   appears.
MASTER                  Mandatory
END                     Mandatory

Sections of an Entry

The following table lists the various sections of a PDB coordinate entry and the records comprising them:

SECTION                  DESCRIPTION                   RECORD TYPE
----------------------------------------------------------------------------
Title                Summary descriptive remarks       HEADER, OBSLTE, TITLE,
                                                       CAVEAT, COMPND, SOURCE,
                                                       KEYWDS, EXPDTA, AUTHOR,
                                                       REVDAT, SPRSDE, JRNL
Remark               Bibliography, refinement          REMARKs 1, 2, 3 & annotations
Primary structure    Peptide and/or nucleotide         DBREF, SEQADV, SEQRES MODRES
                        sequence and the
                        relationship between the PDB
                        sequence and that found in
                        the sequence database(s)
Heterogen            Description of non-standard       HET, HETNAM, HETSYN, FORMUL
                        groups
Secondary structure  Description of secondary          HELIX, SHEET, TURN
                        structure
Connectivity         Chemical connectivity             SSBOND, LINK, HYDBND,
annotation                                             SLTBRG, CISPEP
Miscellaneous        Features within the               SITE
  features              macromolecule
Crystallographic     Description of the                CRYST1
                        crystallographic cell
Coordinate           Coordinate transformation         ORIGXn, SCALEn, MTRIXn, TVECT
transformation          operators
Coordinate           Atomic coordinate data            MODEL, ATOM, SIGATM, ANISOU,
                                                       SIGUIJ, TER, HETATM, ENDMDL
Connectivity         Chemical connectivity             CONECT
Bookkeeping          Summary information,              MASTER, END
                        end-of-file marker

Field Formats

Each record type is presented in a table which contains the division of the records into fields by column number, defined data type, field name or a quoted string which must appear in the field, and field definition. Any column not specified must be left blank.

Each field contains an identified data type that can be validated by a program. These are:

DATA TYPE                  DESCRIPTION
----------------------------------------------------------------------------------
AChar                    An alphabetic character (A-Z, a-z).
Atom                     Atom name
Character                Any non-control character in the ASCII character set or a
                         space.
Continuation             A two-character field that is either blank (for the first
                         record of a set) or contains a two digit number
                         right-justified and blank-filled which counts continuation
                         records starting with 2. The continuation number must be
                         followed by a blank.
Date                     A 9 character string in the form dd-mmm-yy where DD is the
                         day of the month, zero-filled on the left (e.g., 04); MMM is
                         the common English 3-letter abbreviation of the month; and
                         YY is a year in the 20th century. This must represent a
                         valid date.
IDcode                   A PDB identification code which consists of 4 characters,
                         the first of which is a digit in the range 0 - 9; the
                         remaining 3 are alpha-numeric, and letters are upper case
                         only. Entries with a 0 as the first character do not
                         contain coordinate data.
Integer                  Right-justified blank-filled integer value.
Token                    A sequence of non-space characters followed by a colon and a
                         space.
List                     A String that is composed of text separated with commas.
LString                  A literal string of characters. All spacing is significant
                         and must be preserved.
LString(n)               An LString with exactly n characters.
Real(n,m)                Real (floating point) number in the FORTRAN format Fn.m.
Record name              The name of the record: 6 characters, left-justified and
                         blank-filled.
Residue name             One of the standard amino acid or nucleic acids, as listed
                         below, or the non-standard group designation as defined in
                         the HET dictionary. Field is right-justified.
SList                    A String that is composed of text separated with semi-colons.
Specification            A String composed of a token and its associated value
                         separated by a colon.
Specification            A sequence of Specifications, separated by semi-colons.
List
String                   A sequence of characters. These characters may have
                         arbitrary spacing, but should be interpreted as directed
                         below.
String(n)                A String with exactly n characters.
SymOP                    An integer field of from 4 to 6 digits, right-justified, of
                         the form nnnMMM where nnn is the symmetry operator number and
                         MMM is the translation vector.

To interpret a String, concatenate the contents of all continued fields together, collapse all sequences of multiple blanks to a single blank, and remove any leading and trailing blanks. This permits very long strings to be properly reconstructed.