Atomic Coordinate Entry Format Version 3.2
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, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations.
This comprehensive guide describes the "PDB format" used by the members of the worldwide Protein Data Bank (wwPDB; Berman, H.M., Henrick, K. and Nakamura, H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 10, 980 (2003)). Questions should be sent to [email protected]
Information about file formats and data dictionaries can be found at http://wwpdb.org.
Version History:
Version 2.3: The format in which structures were released from 1998 to July 2007.
Version 3.0: Major update from Version 2.3; incorporates all of the revisions used by the wwPDB to integrate uniformity and remediation data into a single set of archival data files including IUPAC nomenclature. See http://www.wwpdb.org/docs.html for more details.
Version 3.1: Minor addenda to Version 3.0, introducing a small number of changes and extensions supporting the annotation practices adopted by the wwPDB beginning in August 2007 including chain ID standardization and biological assembly .
Version 3.15: Minor addenda to Version 3.20, introducing a small number of changes and extensions supporting the annotation practices adopted by the wwPDB beginning in October 2008 including DBREF, taxonomy and citation information.
Version 3.20: Current version, minor addenda to Version 3.1, introducing a small number of changes and extensions supporting the annotation practices adopted by the wwPDB beginning in December 2008 including DBREF, taxonomy and citation information.
September 15 2008, initial version 3.20.
November 15 2008, add examples for Refmac template and coordinate with alternate conformation.
December 24 2008, update REMARK 3 templates/examples, add Norine database in DBREF, update REMARK 500 on chiral center.
February 12 2009, update example in REMARK 210 and record format in NUMMDL.
July 6 2009, update description for REVDAT, DBREF2, MASTER and extend number of columns for AUTHOR, JRNL, CAVEAT, KEYWDS, etc.
December 22, 2009, update CAVEAT and REMARK 265.
April 21, 2010, update REMARK 5 and add BUSTER-TNT template in REMARK 3.
December 06, 2010, update maximum number of atoms for model. Update REMARK 3 with B value type for Refmac template.
March 30, 2011, correct description and examples for FORMUL and CONECT records. Change template in REMARK 630.
Basic Notions of the Format Description
Character Set
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
` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : " < > ?
The use of punctuation characters in the place of alphanumeric characters is discouraged.
The space, and end-of-line:. The end-of-line indicator is system-specific character; some systems may use a carriage return followed by a line feed, others only a line-feed character.
Special Characters
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:
- List
- SList
- Specification List
- Specification
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, "\".
Example - Use of “\” character:
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 is presented in a number of lines. 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 contains a record name, that is left-justified and separated by a blank. The record name must be an exact match to one of the stated record names in this format guide.
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:
- Overview
- Record Format
- Details
- Verification/Validation/Value Authority Control
- Relationship to Other Record Types
- Examples
- Known Problems
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.
One time, single line: There are records that may only appear one time and 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.
NUMMDL Number of models.
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.
One time, multiple lines: 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.
MDLTYP Contains additional annotation pertinent to the coordinates
presented in the entry.
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.
SPLIT List of PDB entries that compose a larger macromolecular
complexes.
SPRSDE List of entries obsoleted from public 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 times, one line: 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 heterogens).
HETATM Atomic coordinate records 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.
SHEET Identification of sheet substructures.
SSBOND Identification of disulfide bonds.
Multiple times, multiple lines: 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. HETNAM Compound name of the heterogens. HETSYN Synonymous compound names for heterogens. SEQRES Primary sequence of backbone residues. SITE Identification of groups comprising important entity sites.
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, ANISOU, 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; they can be structured or free form.
PDB Format Change Policy
The wwPDB will use the following protocol in making changes to the way PDB coordinate entries are represented and archived. The purpose of the policy is to allow ample time for everyone to understand these changes and to assess their impact on existing programs. PDB format modifications are necessary to address the changing needs of PDB users as well as the changing nature of the data that is archived.
- Comments and suggestions will be solicited from the community on specific problems and data representation issues as they arise.
- Proposed format changes will be disseminated through [email protected] and wwpdb.org.
- A 60-day discussion period will follow the announcement of proposed changes. Comments and suggestions must be received within this time period. Major changes that are not upwardly compatible will be allotted up to twice the standard amount of discussion time.
- The wwPDB will then work in consultation with the wwPDB Advisory Committee and the equivalent partner Scientific Advisory Committees to evaluate and reconcile all suggestions. The final decision will be officially announced via [email protected] and wwpdb.org.
- Implementation will follow official announcement of the format change. Major changes will not appear in PDB files earlier than 60 days after the announcement, allowing sufficient time to modify files and programs.
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 entries that have been
replaced by a newer entry.
TITLE Mandatory
SPLIT Optional Mandatory when large macromolecular
complexes are split into multiple PDB
entries.
CAVEAT Optional Mandatory when there are outstanding errors
such as chirality.
COMPND Mandatory
SOURCE Mandatory
KEYWDS Mandatory
EXPDTA Mandatory
NUMMDL Optional Mandatory for NMR ensemble entries.
MDLTYP Optional Mandatory for NMR minimized average
Structures or when the entire polymer
chain contains C alpha or P atoms only.
AUTHOR Mandatory
REVDAT Mandatory
SPRSDE Optional Mandatory for a replacement entry.
JRNL Optional Mandatory for a publication describes
the experiment.
REMARK 0 Optional Mandatory for a re-refined structure
REMARK 1 Optional
REMARK 2 Mandatory
REMARK 3 Mandatory
REMARK N Optional Mandatory under certain conditions.
DBREF Optional Mandatory for all polymers.
DBREF1/DBREF2 Optional Mandatory when certain sequence database
accession and/or sequence numbering
does not fit preceding DBREF format.
SEQADV Optional Mandatory if sequence conflict exists.
SEQRES Mandatory Mandatory if ATOM records exist.
MODRES Optional Mandatory if modified group exists in the
coordinates.
HET Optional Mandatory if a non-standard group other
than water appears in the coordinates.
HETNAM Optional Mandatory if a non-standard group other
than water appears in the coordinates.
HETSYN Optional
FORMUL Optional Mandatory if a non-standard group or
water appears in the coordinates.
HELIX Optional
SHEET Optional
SSBOND Optional Mandatory if a disulfide bond is present.
LINK Optional Mandatory if non-standard residues appear
in a polymer
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.
MODEL Optional Mandatory if more than one model
is present in the entry.
ATOM Optional Mandatory if standard residues exist.
ANISOU Optional
TER Optional Mandatory if ATOM records exist.
HETATM Optional Mandatory if non-standard group exists.
ENDMDL Optional Mandatory if MODEL appears.
CONECT Optional Mandatory if non-standard group appears
and if LINK or SSBOND records exist.
MASTER Mandatory
END Mandatory
Sections of an Entry
The following table lists the various sections of a PDB entry (version 3.2) and the records within it:
SECTION DESCRIPTION RECORD TYPE
-------------------------------------------------------------------------------------
Title Summary descriptive remarks HEADER, OBSLTE, TITLE, SPLIT,
CAVEAT, COMPND, SOURCE, KEYWDS,
EXPDTA, NUMMDL, MDLTYP, AUTHOR,
REVDAT, SPRSDE, JRNL
Remark Various comments about entry REMARKs 0-999
Annotations in more depth than standard
records
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
structure
Connectivity Chemical connectivity SSBOND, LINK, CISPEP
annotation
Miscellaneous Features within the SITE
features macromolecule
Crystallographic Description of the CRYST1
crystallographic cell
Coordinate Coordinate transformation ORIGXn, SCALEn, MTRIXn,
transformation operators
Coordinate Atomic coordinate data MODEL, ATOM, ANISOU,
TER, HETATM, ENDMDL
Connectivity Chemical connectivity CONECT
Bookkeeping Summary information, MASTER, END
end-of-file marker
Field Formats and Data Types
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 the last two digits of the year. 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 List A sequence of Specifications, separated by semi-colons.
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.