(This information is repeated from the Introduction.)
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HEADER Mandatory OBSLTE Optional Mandatory in withdrawn entries.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 Mandatory if structure is deemed incorrect by an outside editorial board. 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 DBREF Optional Mandatory for each peptide chain with a length greater than ten (10) residues, and for nucleic acid. entries that exist in the Nucleic Acid Database (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 SSBOND Optional Mandatory if disulfide bond is present. LINK Optional HYDBND Optional SLTBRG Optional 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
Note that a PDB file existing outside of the PDB official release may contain locally-defined records beginning with "USER". The PDB reserves the right to add new record types (not beginning with "USER"), so programs which read PDB entries should be prepared to read (and ignore) other record types. PDB will follow standard procedures whenever format changes are proposed.
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 and others annotations Primary structure Peptide and/or nucleotide MODRES, DBREF, SEQADV, SEQRES 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