PDBe REST API

This call provides a summary of properties of a PDB entry, such as the title of the entry, list of depositors, date of deposition, date of release, date of latest revision, experimental method, list of related entries in case split entries, etc.

This call provides the details of molecules (or entities in mmcif-speak) modelled in the entry, such as entity id, description, type, polymer-type (if applicable), number of copies in the entry, sample preparation method, source organism(s) (if applicable), etc.

This call provides details of publications associated with an entry, such as title of the article, journal name, year of publication, volume, pages, doi, pubmed_id, etc.
Primary citation is listed first.

This call provides details about publications obtained from both EuroPMC and UniProt. These are articles which cite the primary citation of the entry, or open-access articles which mention the entry id without explicitly citing the primary citation of an entry.

This call provides details of experiment(s) carried out in determining the structure of the entry. Each experiment is described in a separate dictionary.
For X-ray diffraction, the description consists of resolution, spacegroup, cell dimensions, R and Rfree, refinement program, etc.
For NMR, details of spectrometer, sample, spectra, refinement, etc. are included.
For EM, details of specimen, imaging, acquisition, reconstruction, fitting etc. are included.

This call provides URLs of available additional resources for NMR entries. E.g., mapping between structure (PDB) and chemical shift (BMRB) entries.

This call provides a a list of modelled instances of ligands, i.e. 'bound' molecules that are not waters.

This call provides information on carbohydrate polymer entities in each entry.

This call provides a list of modelled instances of modified amino acids or nucleotides in protein, DNA or RNA chains.

This call provides a list of modelled instances of mutated amino acids in proteins in an entry. (Note that at present it does not provide information about mutated nucleotides in RNA or DNA chains, but it would do so in near future.)

This call provides status of a PDB entry (released, obsoleted, on-hold etc) along with some other information such as authors, title, experimental method, etc.

This call provides observed ranges, i.e. segments of structural coverage, of polymeric molecules that are modelled fully or partly.

This call provides observed ranges, i.e. segments of structural coverage, of polymeric molecules in a particular chain.

This call provides details about residue ranges of regular secondary structure (alpha helices and beta strands) found in protein chains of the entry. For strands, sheet id can be used to identify a beta sheet.

This call lists all residues (modelled or otherwise) in the entry, except waters, along with details of the fraction of expected atoms modelled for the residue and any alternate conformers.

This call lists all residues (modelled or otherwise) in the entry, except waters, along with details of the fraction of expected atoms modelled for the residue and any alternate conformers.

This call provides details on binding sites in the entry as per STRUCT_SITE records in PDB files (or mmcif equivalent thereof), such as ligand, residues in the site, description of the site, etc.

This call provides URLs and brief descriptions (labels) for PDB and mmcif files, biological assembly files, FASTA file for sequences, SIFTS cross reference XML files, validation XML files, X-ray structure factor file, NMR experimental constraints files, etc. Please note that these files are also available on https.

This call provides the ratio of observed residues for each chain in each molecule (or entity in mmcif-speak) of a pdb entry. The list of chains within an entity is sorted by observed_ratio (descending order), partial_ratio (ascending order), and number_residues (descending order).

This call provides information for each assembly of a given PDB ID. This information is broken down at the entity level for each assembly. The information given includes the molecule name, type and class, the chains where the molecule occur, and the number of copies of each entity in the assembly.

This call details the statistics for electron density.

This call provides functional annotation of all ligands, i.e. 'bound' molecules that are not waters if available.

This call provides DrugBank annotation of all ligands, i.e. 'bound' molecules that are not waters if available.

This call provides DOI’s for related raw experimental datasets for a PDB entry, including diffraction image data, small-angle scattering data and electron micrographs.