API

The preferred way of accessing M-CSA data is through the public API. The API currently contains two views, one for entries, which includes relevant information at the enzyme level, and another for residues, which lists the catalytic residues and their roles.

Catalytic Residues

To access information about the manually curated catalytic residues in M-CSA use the following link. The data presented in this page can be filtered using the filters below.

https://www.ebi.ac.uk/thornton-srv/m-csa/api/residues/?format=json

To access information about all the catalytic residues in M-CSA including residues found by homology use the following link. Please note that this data cannot be filtered. Since the file is too big to show on the browser (>200mb), the link points to a downloadable file. This file includes all the homologues found in Swiss-Prot and the PDB without regard to the residue conservation or function of the target sequence. This means that the residues in the homologous sequences may be performing a different catalytic function, or no catalytic function at all. Residues with 'null' fields could not be aligned to the target sequence.

https://www.ebi.ac.uk/thornton-srv/m-csa/api/homologues_residues.json

Entry data

To access general information about M-CSA entries, including residue and mechanism information, please use the link below.

https://www.ebi.ac.uk/thornton-srv/m-csa/api/entries/?format=json

Filters

Both views can be filtered by EC, UniProt or M-CSA id, to show only relevant entries or residues. The filters are applied by adding the relevant option to the url. Some examples are given below:

Show Enzyme Mechanisms in your website

We have created a Polymer web component that can be easily embedded in any website to show enzyme mechanism information. The filters described above can be used to select which enzymes mechanisms are shown. This minimal page shows the web component and how to embedded it.


 
Please note that the flat files provided below are not being updated anymore. Please use the API instead.
 

Flat Files

M-CSA curated data flat-file

This file lists all the residues, cofactors, reactants and products for all the entries in M-CSA. Reference UniProt and PDB IDs are given, as well as the reference reaction EC number. Residues are identified by their chain and residue ID in the biological assembly of the reference PDB. Cofactors are identified by their name, HET code, KEGG compound ID, and ChEBI ID. Reactants and products are identified by their KEGG compound ID and ChEBI ID. Roles are grouped in three categories: reactant, interaction, and spectator. The parent role is given when available, it is derived from the EMO (Enzyme Mechanism Ontology)

curated_data.csv

'CSA Style' files with list of curated catalytic residues

Curated catalytic residues

Each line of this file corresponds to a catalytic residue in the M-CSA. Only catalytic residues manually annotated in the reference PDB are included. This file matches the style of the flat file provided by the CSA v2.0 website. Resid and chain names are the ones found in the first biological assembly defined by PDBe, which is available as a cif file for each PDB entry. Function location corresponds to the portion of the residue important for catalysis: S - side chain; N - main chain amide or main chain N-terminus; C - main chain carbonyl or main chain C-terminus; U - post translation modification; M - main chain.

literature_pdb_residues.csv
Curated catalytic residues with their roles annotated

Each line of this file corresponds to a role done by a catalytic residue. If a catalytic residue has more than one role, it appears on more than one line. The roles are grouped in three categories: reactant, interaction, and spectator. The parent role is given when available, it is derived from the EMO (Enzyme Mechanism Ontology)

literature_pdb_residues_roles.csv