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.
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.
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:
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
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.
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.
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.
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
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
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.