(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OBSLTE Optional Mandatory in withdrawn entries.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