Programmatic access

Retrieving entries by Id

Retrieve by PDB code to get data about metal sites embedded in the structure:
E.g. :

Retrieve by MetalPDB site code:
E.g. :

Retrieve by UniProt accession number to get data about the protein metal sites :
E.g. :

Retrieving entries via query

You can search by one or more key and define one or more columns to retrieve. The sintax is key:value.
E.g. :,uniprot,ec_number,metal,ligands

To build a complex query join the keys with comma.
E.g. :,metal:Zn&columns=pfam,metal,ligands,donors

If you don't specify the columns of interest will be retrieved all of them.
E.g. :,metal:Zn

Keys allowed for queries

Key Description Exemple
Macromolecule Features
organism Organism name api?query=organism:Homo sapiens
molecule Macromolecule name api?query=molecule:Carbonic anhydrase 2
ec_number EC Number api?query=ec_number:
pdb PDB structure code api?query=pdb:12ca
uniprot Uniprot accession number api?query=uniprot:P00918
Site Features
site_type Site Type (Nuclearity) api?query=site_type:tetranuclear
pfam Pfam domain name api?query=pfam:Carb_anhydrase
cath Cath Id api?query=cath:
scop Scop Id api?query=scop:b.74.1.1
representative Search only among representative sites of families. api?query=representative:true
Metal Features
metal Metal symbol api?query=metal:Zn
ligands Type of metal ligand residue api?query=ligands:His
geometry Metal geometry. The value must be a geometry name (see Geometry) api?query=geometry:oct
coordination Metal coordination number api?query=coordination:3
donors Type of donor atom of metal ligand residues api?query=donors:S

Columns to retrieve

Field Type Description Inner Fields Exemple
Macromolecule Features
organism String Organism name None api?query=pdb:12ca&columns=organism
molecule String Macromolecule name None api?query=pdb:12ca&columns=molecule
ec_number Array of Strings EC Number None api?query=pdb:12ca&columns=ec_number
pdb_code String PDB code None api?query=pdb:12ca&columns=pdb_code
uniprot String Uniprot accession number None api?query=pdb:12ca&columns=uniprot
Site Features
site_type Integer Site Type (Nuclearity) None api?query=pdb:12ca&columns=site_type
pfam Array of Strings Pfam domain name(s) None api?query=pdb:12ca&columns=pfam
cath Array of Strings Cath Id(s) None api?query=pdb:12ca&columns=cath
scop Array of Strings Scop Id(s) None api?query=pdb:12ca&columns=scop
is_representative Boolean For each result retrieve if it is the representative site of its family. None api?query=pdb:12ca&columns=is_representative
Metal Features
metal Array of Objects Data about metal(s) bound by the structure symbol, atom_pdb_number, name, residue_pdb_number api?query=pdb:12ca&columns=metal
Metal Features Optional Parameters
pattern String Metal pattern for each metal bound by the structure None query=pdb:12ca&columns=pattern
geometry String Metal geometry for each metal bound by the structure None api?query=pdb:12ca&columns=geometry
coordination Integer Metal coordination number for each metal bound by the structure None api?query=pdb:12ca&columns=coordination
ligands Array of Objects Data about each ligand residue for each metal bound by the structure residue, chain, residue_pdb_number api?query=pdb:12ca&columns=ligands
donors Array of Objects Data about each donor atom of ligand residues for each metal bound by the structure symbol, atom, atom_pdb_number, distance (from metal) api?query=pdb:12ca&columns=donors