Christoph at 06:45, 25 April 2007

2007-04-25T06:45:42Z

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The '''Protein Data Bank''' ('''PDB''') is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by [[:Category:Crystallography|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
<pre>
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.
</pre>
# 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 <code>ATOM/HETATM</code> 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 <code>ATOM</code> records are compared to the corresponding sequence database. Residue discrepancies appear in the <code>SEQADV</code> record. Missing atoms are annotated in the remarks. <code>HETATM</code> records are formatted in the same way as <code>ATOM</code> records. The sequence implied by <code>ATOM</code> records must be identical to that given in <code>SEQRES</code>, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in <code>SEQRES</code>.

*Example
<pre>
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
</pre>

*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., <code>A, C, G, T, U</code>).

==External links==
*[http://www.rcsb.org/ RCSB PDB]
*[http://www.wwpdb.org/documentation/format23/v2.3.html Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description] — version 2.3; 1998-07-09.
*[[wikipedia:Protein Data Bank]]
*[[wikipedia:Protein Data Bank (file format)]]

[[Category:Bioinformatics]]
[[Category:Crystallography]]

PDB - Revision history

Christoph at 06:45, 25 April 2007