MMB Data repository API Interface

Statistics

/info[.xml|.json]

PDB/Uniprot data repository information (default json)

Protein Data Bank

/pdb/{id}/entry[.xml|.json]	PDB full entry metadata: Ascession Date, Experiment type, resolution, compound, compound type, authors, sources, chain ids, ligand data, remarks, chain sequences, sequence clusters, best SwissProt hits, uniprot entry (default json). Individual fields can be recovered, completing the URI
Parameters
Usage example	/pdb/2ki5/entry?[.xml|.json] SwissProt Hit on chain 0 (A) sequence. /pdb/2ki5/entry/chains/0/swpHit/idHit
/pdb/{id}[_bn{n}]/headers[.gz]	Headers from PDB file
Options	{id}_bn{n}: Biounit {n} instead of assymetric unit Format: .gz: Compressed output
Usage example	/pdb/2ki5/headers[.gz]
/pdb/{id}[_chainId]/sequence[.gz] /pdb/{id}[_chainId].fasta	FASTA formatted sequence from PDB entry
Options	{id}_{chain_id} Only selected chain (case sensitive). .gz: Compressed output
Usage example	/pdb/2ki5/sequence?[.gz] /pdb/2ki5.fasta
/pdb/{id}[_chainId]/clusters[.xml|.json]/	PDB ids of sequence cluster reference structures
Options	{id[_chain_id]} Only selected chain .xml|.json) XML or Json format selection (default tabular text).
Usage example	/pdb/2ki5[_A]/clusters[.xml|.json]
/pdb/{id[_chainId]}/clusters/{clusterId}[.xml|.json]	Members of sequence cluster
Options	{id_chainId} Only selected chain .xml|.json) XML or Json format selection (default tabular text).
Usage example	/pdb/2ki5[_A]/clusters/cl-90[.xml|.json]
/pdb/{id[_bn{n}}[.pdb|.cif|.json|.xml][.gz] /pdb/{id[_bn{n}}/coords[.gz]	PDB structure coordinates (Default: PDB Format)
Parameters (PDB/CIF format)	{id_bnN} Show Biounit N instead of the Assymetric Unit The following parameters add cumulative restrictions starting from the complete PDB: noheaders[=1] Skip PDB headers (implicit in the following filters) noanisou[=1] Skip ANISOU records noalt[=1] Skip all alternative atom but A (label is retained in the output) alt=X Skip all alternative atom but those labelled as X (label is retained in the output) nowat[=1] Skip water molecules group=(ATOM | HETATM) PDB label selection. (HETATM includes CONECT). "!" negates. Comma separated values accepted. groupRes=[!](POLAR | APOLAR | NUC | PROT) Residue type selection. "!" negates groupAt=[!](POLAR | APOLAR | NOH | BACK | NABACK) Atom type selection, "!" negates filter=[!][RES]nres:chain.atom/model Atom filter using J(s)Mol format ("!" negates selection) Format: .gz: Compressed output
Parameters (json|XML formats)	{id_bnN} Show Biounit N instead of the Assymetric Unit atoms=(no|none|block|full) Format for atom coordinates: No, none: No atom coordinates, block: a single block in mmCIF format (Default), full: complete json/xml structure (may fail for large structures)
Usage example	Standard gzipped PDB file for 2ki5 /pdb/2ki5.gz Coordinates for CA atoms of polar residues from B subunit of 2ki5. /pdb/2ki5/coords/?groupRes=POLAR&filter=:B.CA Coordinates of POLAR atoms from a sequence fragment (100-110) of 2ki5. /pdb/2ki5/coords/?groupAt=POLAR&filter=100-110 Coordinates of POLAR atoms from ASP residues in a sequence fragment (100-110) of 2ki5. /pdb/2ki5/coords/?groupAt=POLAR&filter=[ASP]100-110 Coordinates of terminal OD* from ASP residues of 2ki5. /pdb/2ki5/coords/?filter=[ASP]:.OD*
/pdb/	List of PDB entries filtered by parameters
Parameters	resmin=value Minimum value for resolution (XRAY only) resmax=value Maximum value for resolution (XRAY only) qcompType=(prot, nuc, prot-nuc, carb, other) Compound types. Comma separated values (default any) qexpType=(ELECTRON_CRYSTALLOGRAPHY, ELECTRON_MICROSCOPY,FLUORESCENCE_TRANSFER, INFRARED, NEUTRON_DIFRACCTION, NMR, SOLID-STATE_NMR, X-RAY) Type of Experiment. Comma separated values (default any) For available options for qcompType, and qexpType use /pdb/info query=txt Text query queryOn=(header, compound, sources, authors) Fields for text query (default all) sequence=seq Sequence match molTy=(protein | na) Sequence type (required when sequence) seqType=(exact | regex) Type of sequence match (exact | regular expression (default)) sort=(_id | header | compType | expType | resol) Ordering (ascending)
Usage example	List of PDB entries corresponding to "kinase" obtained by X-RAY with resolution better than 1.8 A /pdb/?query=kinase&resmax=1.8&qexpType=X-RAY&sort=resol List of PDB entries corresponding to protein - nucleic Acid complexes where NA sequence contains "ACGT", tab format /pdb/?qcompType=prot-nuc&sequence=ACGT&molTy=na&seqType=regex
/pdbMonomer/{id}[.gz]/ /pdbMonomer/{id}/coords/	Monomer coordinates (PDB Format)
Parameters	idPDB={id} Get monomer from selected PDB entry, otherwise first entry available is given groupAt=[!](POLAR | APOLAR | NOH) Atom type selection, "!" negates filter=[!][RES]nres:chain.atom/model Atom filter using J(s)Mol format ("!" negates selection) gzip=1 | .gz: Compressed output
Usage example	/pdbMonomer/AC2[.gz]
/pdbMonomer/{id}/entry[.xml | .json]	Monomer data.Individual fields can be recovered, completing the URI
Parameters	[.xml | .json]: Output Format
Usage example	/pdbMonomer/AC2/entry[.xml|.json]

Uniprot

uniprot/{id}[.xml | .json]/ uniprot/{id}/entry[.xml | .json]	Uniprot entry: Accession, Swp id, headers, DB crossrefs, Sequence Features, Known variants and isoforms. Individual fields can be recovered, completing the URI
Parameters
Usage example	uniprot/P03176/entry[.xml|.json]
uniprot/{id}/entry/{field}/	Uniprot entry specific field (see /entry/ for examples
Parameters	fmt: (xml | json). Output format (default xml).
Usage example	uniprot/P03176/entry/dbxref/?[fmt=xml|json]
uniprot/{id}/sequence/ uniprot/{id}/entry/fasta/ uniprot/{id}.fasta	FASTA formatted sequence from UniprotKb entry
Parameters	isoforms=1 Include annotated isoforms
Usage example	uniprot/P03176.fasta/?[isoforms=1]

Enzyme

/enzyme/{id}[.xml | .json]/ /enzyme/{id}/entry[.xml | .json]	Enzyme entry: Comment, alt names, description, UniprotIds. Individual fields can be recovered completing the URI.
Parameters	Format: (.xml | .json). Output format (default json).
Usage example	/enzyme/1.1.1.1/entry?[.xml|.json]
/enzyme/{id}/entry/{field}[.xml | .json]/	Enzyme entry specific field (see /entry/ for examples
Parameters	fmt: (xml | json). Output format (default json).
Usage example	/enzyme/1.1.1.1/entry/uniprotIds?[.xml|.json]