2GKE
Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008837 | molecular_function | diaminopimelate epimerase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016853 | molecular_function | isomerase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ZDP A 700 |
| Chain | Residue |
| A | ASN11 |
| A | ASN190 |
| A | GLU208 |
| A | ARG209 |
| A | CYS217 |
| A | GLY218 |
| A | SER219 |
| A | GLN44 |
| A | ASN64 |
| A | VAL70 |
| A | GLN72 |
| A | CYS73 |
| A | GLY74 |
| A | ASN75 |
| A | ASN157 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 694 |
| Chain | Residue |
| A | THR26 |
| A | THR29 |
| A | GLU124 |
| A | ASN133 |
| A | LYS134 |
| A | PHE135 |
| A | LEU274 |
| A | HOH310 |
| A | HOH497 |
| A | HOH591 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ACY A 695 |
| Chain | Residue |
| A | TYR139 |
| A | ILE140 |
| A | ARG184 |
| A | HOH340 |
| A | HOH373 |
| A | HOH493 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE ACY A 696 |
| Chain | Residue |
| A | GLU69 |
| A | SER71 |
| A | GLN100 |
| A | LYS101 |
| A | HIS256 |
| A | HOH319 |
| A | HOH492 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ACY A 697 |
| Chain | Residue |
| A | GLU187 |
| A | ARG188 |
| A | GLY255 |
| A | HOH674 |
Functional Information from PROSITE/UniProt
| site_id | PS01326 |
| Number of Residues | 15 |
| Details | DAP_EPIMERASE Diaminopimelate epimerase signature. NaDGSevsqCGNGaR |
| Chain | Residue | Details |
| A | ASN64-ARG78 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"6122","lastPage":"6123","volume":"122","journal":"J. Am. Chem. Soc.","title":"Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase.","authors":["Koo C.W.","Sutherland A.","Vederas J.C.","Blanchard J.S."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001193t"}]}},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"6122","lastPage":"6123","volume":"122","journal":"J. Am. Chem. Soc.","title":"Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase.","authors":["Koo C.W.","Sutherland A.","Vederas J.C.","Blanchard J.S."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001193t"}]}},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 7 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16723397","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2GKJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Site: {"description":"Could be important to modulate the pK values of the two catalytic cysteine residues","evidences":[{"source":"PubMed","id":"9843410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1BWZ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | Site: {"description":"Important for dimerization","evidences":[{"source":"UniProtKB","id":"P0A6K1","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1bwz |
| Chain | Residue | Details |
| A | GLU208 | |
| A | CYS73 | |
| A | CYS217 | |
| A | HIS159 |
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 334 |
| Chain | Residue | Details |
| A | CYS73 | hydrogen bond acceptor, proton acceptor |
| A | HIS159 | activator, electrostatic stabiliser |
| A | GLU208 | activator, electrostatic stabiliser |
| A | CYS217 | hydrogen bond donor, proton donor |
| A | GLY220 | electrostatic stabiliser, hydrogen bond donor |
