1YBQ
Crystal structure of Escherichia coli isoaspartyl dipeptidase mutant D285N complexed with beta-aspartylhistidine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006508 | biological_process | proteolysis |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008237 | molecular_function | metallopeptidase activity |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0008798 | molecular_function | beta-aspartyl-peptidase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016810 | molecular_function | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006508 | biological_process | proteolysis |
| B | 0008233 | molecular_function | peptidase activity |
| B | 0008237 | molecular_function | metallopeptidase activity |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0008798 | molecular_function | beta-aspartyl-peptidase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016810 | molecular_function | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN A 391 |
| Chain | Residue |
| A | HIS68 |
| A | HIS70 |
| A | ASN285 |
| A | ZN392 |
| A | BDH393 |
| A | HOH508 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN A 392 |
| Chain | Residue |
| A | ZN391 |
| A | BDH393 |
| A | HOH508 |
| A | TYR137 |
| A | HIS201 |
| A | HIS230 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE BDH A 393 |
| Chain | Residue |
| A | GLY74 |
| A | GLY75 |
| A | GLU77 |
| A | GLY105 |
| A | THR106 |
| A | TYR137 |
| A | ARG169 |
| A | HIS201 |
| A | ARG233 |
| A | ASN285 |
| A | GLY288 |
| A | SER289 |
| A | PRO291 |
| A | ZN391 |
| A | ZN392 |
| A | HOH414 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 391 |
| Chain | Residue |
| B | HIS68 |
| B | HIS70 |
| B | KCX162 |
| B | ASN285 |
| B | ZN392 |
| B | BDH393 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 392 |
| Chain | Residue |
| B | TYR137 |
| B | KCX162 |
| B | HIS201 |
| B | HIS230 |
| B | ZN391 |
| B | BDH393 |
| site_id | AC6 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE BDH B 393 |
| Chain | Residue |
| B | HIS70 |
| B | GLY74 |
| B | GLY75 |
| B | GLU77 |
| B | GLY105 |
| B | THR106 |
| B | TYR137 |
| B | KCX162 |
| B | ARG169 |
| B | HIS201 |
| B | HIS230 |
| B | ARG233 |
| B | ASN285 |
| B | SER289 |
| B | PRO291 |
| B | ZN391 |
| B | ZN392 |
| B | HOH483 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"12946361","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"12718528","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12946361","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15882050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16289685","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 10 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"12718528","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"12946361","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"15882050","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Binding site: {"description":"via carbamate group","evidences":[{"source":"PubMed","id":"12718528","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12946361","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15882050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16289685","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"PubMed","id":"12718528","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12946361","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15882050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16289685","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | a catalytic site defined by CSA, PubMed 15882050 |
| Chain | Residue | Details |
| A | ASN285 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | a catalytic site defined by CSA, PubMed 15882050 |
| Chain | Residue | Details |
| B | ASN285 |
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 172 |
| Chain | Residue | Details |
| B | HIS68 | metal ligand |
| B | HIS70 | metal ligand |
| B | KCX162 | metal ligand |
| B | SER205 | metal ligand |
| B | ASN234 | metal ligand |
| B | SER289 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
