PROCHECK Operating Manual

Appendix B - Brookhaven PDB file format

The table below shows the Brookhaven file format for the coordinate records (ie ATOM and HETATM) of your PDB file. Each record holds the coordinates and other details of a single atom.

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Field |    Column    | FORTRAN |                                         
  No. |     range    | format  | Description                                   
---------------------------------------------------------------------------
   1. |    1 -  6    |   A6    | Record ID (eg ATOM, HETATM)       
   2. |    7 - 11    |   I5    | Atom serial number                            
   -  |   12 - 12    |   1X    | Blank                                         
   3. |   13 - 16    |   A4    | Atom name (eg " CA " , " ND1")   
   4. |   17 - 17    |   A1    | Alternative location code (if any)            
   5. |   18 - 20    |   A3    | Standard 3-letter amino acid code for residue 
   -  |   21 - 21    |   1X    | Blank                                         
   6. |   22 - 22    |   A1    | Chain identifier code                         
   7. |   23 - 26    |   I4    | Residue sequence number                       
   8. |   27 - 27    |   A1    | Insertion code (if any)                       
   -  |   28 - 30    |   3X    | Blank                                         
   9. |   31 - 38    |  F8.3   | Atom's x-coordinate                         
  10. |   39 - 46    |  F8.3   | Atom's y-coordinate                         
  11. |   47 - 54    |  F8.3   | Atom's z-coordinate                         
  12. |   55 - 60    |  F6.2   | Occupancy value for atom                      
  13. |   61 - 66    |  F6.2   | B-value (thermal factor)                    
   -  |   67 - 67    |   1X    | Blank                                         
  14. |   68 - 70    |   I3    | Footnote number                               
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Example:-

Four sample records are shown below:-

         1         2         3         4         5         6        
12345678901234567890123456789012345678901234567890123456789012345678
--------------------------------------------------------------------
ATOM   1751  N   GLY C 250      32.286   1.882  43.206  1.00 22.00
ATOM   1752  CA  GLY C 250      32.365   1.086  41.969  1.00 21.39
ATOM   1753  C   GLY C 250      31.538   1.735  40.864  1.00 20.79
ATOM   1754  O   GLY C 250      30.621   2.527  41.152  1.00 21.58

NMR Ensembles

For NMR ensembles the coordinates of each model should be preceded by a MODEL record, and terminated by an ENDMDL record. The format of the former is ('MODEL',5X,I4), where the I4 holds the model number. For example:-

MODEL        1
^^^^^^^^^^^^^^
MODELxxxxxIIII