Header of PDB file

From Proteopedia

Current revision

PDB files contain atomic coordinates plus additional annotations in a header section. The header section is everything before the first record (line) beginning with MODEL or ATOM or HETATM. Here is an excerpt of the header for 1ijw:

HEADER    DNA BINDING PROTEIN/DNA                 30-APR-01   1IJW              

TITLE     TESTING THE WATER-MEDIATED HIN RECOMBINASE DNA RECOGNITION            

TITLE    2 BY SYSTEMATIC MUTATIONS.                                             

COMPND    MOL_ID: 1;                                                            

COMPND   2 MOLECULE: 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-           

COMPND   3 3';                                                                  

COMPND   4 CHAIN: A;                                                            

COMPND   5 ENGINEERED: YES;                                                     
.
.
.
CRYST1   85.749   81.136   44.596  90.00  90.00  90.00 C 2 2 21      8          

ORIGX1      1.000000  0.000000  0.000000        0.00000                         

ORIGX2      0.000000  1.000000  0.000000        0.00000                         

ORIGX3      0.000000  0.000000  1.000000        0.00000                         

SCALE1      0.011662  0.000000  0.000000        0.00000                         

SCALE2      0.000000  0.012325  0.000000        0.00000                         

SCALE3      0.000000  0.000000  0.022424        0.00000

The header section should not be confused with the HEADER record, which is the first line in a PDB file, and always a single line. Here is the HEADER record for 1ijw:

HEADER    DNA BINDING PROTEIN/DNA                 30-APR-01   1IJW

The header section for an X-ray crystallographic model specifies important information including a TITLE, the type and source of the molecule (COMPND, SOURCE), the method of structure determination (EXPDTA), the publication (AUTHOR, JRNL, REMARK 1), experimental details in a series of REMARK records, the biological assembly (REMARK 350), missing residues (REMARK 465), geometry and stereochemistry anomalies (REMARK 500), database links such as the UniProt identifier (DBREF), discrepancies in sequences (SEQADV), sequences of the modeled polymers (SEQRES), names of hetero compounds (HETNAM, HETSYN), secondary structure (HELIX, SHEET), and a description of the crystallographic unit cell (CRYST, ORIGX, SCALE), among other things.

Example

Right click these links to open in a new browser tab:

• Header section of PDB file 1hxw.
• Entire PDB file 1hxw. Following the header section are the ATOM and HETATM records.

Methods for Viewing the Header Section

In Proteopedia, at the page titled with the PDB code (for example 1hxw):

• Click FirstGlance. In FirstGlance, scroll down and click Show More Details, then click View PDB File.
• Click OCA. There, under Data retrieval, Asymmetric unit, click [header only].
• Click PDBe. There, click View (right side of page), and then PDB header.
• Click RCSB. There, click Display Files, PDB Format (Header).