Overview

The Coordinate Server is a fast, web-based tool for returning a subset of mmCIF coordinate data for a PDB entry held in the PDB archive. The server can return just the relevant portions of the structure specified in the query, for example, a 5 Ångstrom radius around the ligand binding site including symmetry mates. As it only returns the requested data, it greatly reduces the transmission time and time required to parse and manipulate an entire file.
In addition, it can also perform various calculations on the data, such as generating assemblies. The results of these calculations are then served in mmCIF format. mmCIF format is the archival format for the Protein Data Bank and there are numerous parsers and software in the structural biology domain that can readily consume this data format (See the demo page for an example using LiteMol)

How it works

Any structure in the PDB archive can be queried with a simple GET request to a URL, with each endpoint in the URL corresponding to a specific query. Parameters can be passed to the query as parameters in the URL. For a list of available queries and corresponding parameters, as well as example URLs, please refer to the documentation section.

Advantages

  • Focus only on the relevant data, no need to download and parse complete structure files, for example the mmCIF file for 3j3q is reduced from 254MB to 119MB when downloading just the backbone atoms.
  • Most common tasks performed for you, e.g., assembly generation, finding backbone, sidechain or HETATM records
  • The result is in mmCIF, the standard format used by the wwPDB which many current viewers and tools work with.

Released versions

The following versions are released and available :

  • version 1.3.12

Contributors

PDBe NCBR