Retrieve by PDB code to get data about metal sites embedded in the structure:
E.g. : http://metalpdb.cerm.unifi.it/api?query=pdb:12ca
Retrieve by MetalPDB site code:
E.g. : http://metalpdb.cerm.unifi.it/api?query=site:12ca_2
Retrieve by UniProt accession number to get data about the protein metal sites :
E.g. : http://metalpdb.cerm.unifi.it/api?query=uniprot:P00918
You can search by one or more key and define one or more columns to retrieve. The sintax is key:value.
E.g. : http://metalpdb.cerm.unifi.it/api?query=pdb:12ca&columns=pfam,uniprot,ec_number,metal,ligands
To build a complex query join the keys with comma.
E.g. : http://metalpdb.cerm.unifi.it/api?query=pdb:12ca,metal:Zn&columns=pfam,metal,ligands,donors
If you don't specify the columns of interest will be retrieved all of them.
E.g. : http://metalpdb.cerm.unifi.it/api?query=pdb:12ca,metal:Zn
| 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:4.2.1.1 |
| 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:3.10.200.10 |
| 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 |
| 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 | |