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Protein Data Bank Contents Guide:
Atomic Coordinate Entry Format Description
Version 3.30
Document Published by the wwPDB
This format complies with the PDB Exchange Dictionary (PDBx)
http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html.
©2008 wwPDB
PDB File Format v. 3.3
Page i
Table of Contents
1. Introduction ...................................................................................................................................1  
Basic Notions of the Format Description ............................................................................................ 3  
Record Format.................................................................................................................................... 5  
Types of Records ............................................................................................................................... 6  
PDB Format Change Policy................................................................................................................ 9  
Order of Records .............................................................................................................................. 10  
Sections of an Entry ......................................................................................................................... 12  
Field Formats and Data Types ......................................................................................................... 14  
2. Title Section ................................................................................................................................16  
HEADER........................................................................................................................................... 16  
OBSLTE ........................................................................................................................................... 19  
TITLE ................................................................................................................................................ 21  
SPLIT (added) .................................................................................................................................. 22  
CAVEAT ........................................................................................................................................... 23  
COMPND (updated) ......................................................................................................................... 24  
SOURCE (updated) .......................................................................................................................... 26  
KEYWDS .......................................................................................................................................... 31  
EXPDTA (updated) ........................................................................................................................... 33  
NUMMDL (added) ............................................................................................................................ 35  
MDLTYP (added).............................................................................................................................. 36  
AUTHOR .......................................................................................................................................... 38  
REVDAT (updated) ........................................................................................................................... 40  
SPRSDE ........................................................................................................................................... 42  
JRNL (updated) ................................................................................................................................ 44  
REMARK .......................................................................................................................................... 52  
REMARKs 0-5......................................................................................................................... 52  
REMARK 0 (added), Re-refinement notice ............................................................................... 52  
REMARK 1 (updated), Related publications ............................................................................. 54  
REMARK 2 (updated), Resolution ............................................................................................ 60  
REMARK 3 (updated), Final refinement information ................................................................. 61  
Refinement using X-PLOR ........................................................................................................ 62  
Refinement using CNS .............................................................................................................. 64  
Refinement using CNX .............................................................................................................. 66  
Refinement using REFMAC ...................................................................................................... 68  
Refinement using NUCLSQ ...................................................................................................... 76  
Refinement using SHELXL ....................................................................................................... 80  
Refinement using TNT/BUSTER ............................................................................................... 82  
Refinement using PHENIX ........................................................................................................ 85  
Refinement using BUSTER-TNT .............................................................................................. 93  
Example for Solution Scattering ................................................................................................ 98  
Non-diffraction studies .............................................................................................................. 98  
REMARK 4 (updated), Format .................................................................................................. 99  
REMARK 5 (updated), Obsolete Statement .............................................................................. 99  
PDB File Format v. 3.3
Page ii
REMARKs 6 - 99................................................................................................................... 100  
REMARK 100 (updated), Deposition or Processing Site ...................................................... 100  
REMARKs 200-265, Experimental Details............................................................................ 101  
REMARK 200 (updated), X-ray Diffraction Experimental Details ............................................ 101  
REMARK 205, Fiber Diffraction, Fiber Sample Experiment Details ........................................ 104  
REMARKs 210 and 215/217, NMR Experiment Details .......................................................... 104  
REMARK 230, Neutron Diffraction Experiment Details ........................................................... 106  
REMARK 240 (updated), Electron Crystallography Experiment Details ................................. 109  
REMARK 245 (updated), Electron Microscopy Experiment Details ........................................ 111  
REMARK 247, Electron Microscopy details ............................................................................ 113  
REMARK 250, Other Type of Experiment Details ................................................................... 113  
REMARK 265, Solution Scattering Experiment Details .......................................................... 114  
REMARKs 280-290, Crystallographic Details ....................................................................... 116  
REMARK 280, Crystal ............................................................................................................. 116  
REMARK 285, CRYST1 .......................................................................................................... 116  
REMARK 290, Crystallographic Symmetry ............................................................................. 117  
REMARK 300 (updated), Biomolecule .................................................................................... 118  
REMARK 350 (updated), Generating the Biomolecule ........................................................... 120  
Example – When software predicts multiple quaternary assemblies ...................................... 122  
REMARK 375 (updated), Special Position .............................................................................. 124  
REMARK 400, Compound ...................................................................................................... 124  
REMARK 450, Source ............................................................................................................ 126  
REMARK 465 (updated), Missing residues ............................................................................. 126  
REMARK 470 (updated), Missing Atom(s) .............................................................................. 127  
REMARK 475 (added), Residues modeled with zero occupancy ........................................... 128  
REMARK 480 (added), Polymer atoms modeled with zero occupancy .................................. 129  
REMARK 500 (updated), Geometry and Stereochemistry ...................................................... 130  
REMARK 525 (updated), Distant Solvent Atoms .................................................................... 136  
REMARK 600, Heterogen ....................................................................................................... 136  
REMARK 610, Non-polymer residues with missing atoms ..................................................... 138  
REMARK 615, Non-polymer residues containing atoms with zero occupancy ....................... 138  
REMARK 620 (added), Metal coordination ............................................................................. 139  
REMARK 630 (added), Inhibitor Description ........................................................................... 141  
REMARK 650, Helix ................................................................................................................ 142  
REMARK 700, Sheet .............................................................................................................. 143  
REMARK 800 (updated), Important Sites ............................................................................... 145  
REMARK 999, Sequence ........................................................................................................ 147  
3. Primary Structure Section .........................................................................................................148  
DBREF (standard format) ............................................................................................................... 148  
DBREF1 / DBREF2 (added) ........................................................................................................... 151  
SEQADV......................................................................................................................................... 152  
SEQRES (updated) ........................................................................................................................ 155  
MODRES (updated) ....................................................................................................................... 157  
4. Heterogen Section (updated) ....................................................................................................159  
HET ................................................................................................................................................ 159  
HETNAM ........................................................................................................................................ 161  
PDB File Format v. 3.3
Page iii
HETSYN ......................................................................................................................................... 163  
FORMUL ........................................................................................................................................ 164  
5. Secondary Structure Section.....................................................................................................166  
HELIX ............................................................................................................................................. 166  
SHEET............................................................................................................................................ 168  
6. Connectivity Annotation Section ...............................................................................................171  
SSBOND (updated) ........................................................................................................................ 171  
LINK (updated) ............................................................................................................................... 173  
CISPEP .......................................................................................................................................... 175  
7. Miscellaneous Features Section ...............................................................................................177  
SITE................................................................................................................................................ 177  
8. Crystallographic and Coordinate Transformation Section .........................................................179  
CRYST1 ......................................................................................................................................... 179  
ORIGXn .......................................................................................................................................... 181  
SCALEn .......................................................................................................................................... 182  
MTRIXn .......................................................................................................................................... 184  
9. Coordinate Section ....................................................................................................................185  
MODEL ........................................................................................................................................... 185  
ATOM ............................................................................................................................................. 187  
ANISOU .......................................................................................................................................... 190  
TER ................................................................................................................................................ 192  
HETATM ......................................................................................................................................... 194  
ENDMDL ........................................................................................................................................ 196  
10. Connectivity Section ................................................................................................................197  
CONECT ........................................................................................................................................ 197  
11. Bookkeeping Section ..............................................................................................................199  
MASTER......................................................................................................................................... 199  
END ................................................................................................................................................ 201  
PDB File Format v. 3.3
Page 1
1. 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 info@wwpdb.org
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: 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.

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