PDB
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain, and can be accessed for free.
ATOM coordinates format overview
The ATOM records present the atomic coordinates for standard residues (see http://deposit.pdb.org/public-component-erf.cif). They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.
- Record Format
COLUMNS DATA TYPE FIELD DEFINITION
------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in
Angstroms
39 - 46 Real(8.3) y Orthogonal coordinates for Y in
Angstroms
47 - 54 Real(8.3) z Orthogonal coordinates for Z in
Angstroms
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.
- ATOM records for proteins are listed from amino to carboxyl terminus.
- Nucleic acid residues are listed from the 5' to the 3' terminus.
- No ordering is specified for polysaccharides.
- The list of ATOM records in a chain is terminated by a TER record.
- If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.
- If an atom is provided in more than one position, then a non-blank alternate location indicator must be used as the alternate location indicator for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator.
- For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/ HETATM list uses the following general rules:
- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
- The insertion code is commonly used in sequence numbering
- If the depositor provides the data, then the isotropic B value is given for the temperature factor.
- If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
- Columns 77 - 78 contain the atom's element symbol (as given in the periodic table), right-justified.
- Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases these are blank.
- Verification/Validation/Value Authority Control
PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format.
- Relationships to Other Record Types
The ATOM records are compared to the corresponding sequence database. Residue discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES.
- Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 N
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85 C
ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34 C
ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65 O
ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88 C
ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41 C
ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64 C
ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11 C
ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58 C
ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 C
- Known Problems
No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U).
