2PZ0
Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0006629 | biological_process | lipid metabolic process |
| A | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| A | 0008889 | molecular_function | glycerophosphodiester phosphodiesterase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0006629 | biological_process | lipid metabolic process |
| B | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| B | 0008889 | molecular_function | glycerophosphodiester phosphodiesterase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CA A 501 |
| Chain | Residue |
| A | GLU44 |
| A | ASP46 |
| A | GLU119 |
| A | HOH503 |
| A | HOH628 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CA B 502 |
| Chain | Residue |
| B | HOH607 |
| B | GLU44 |
| B | ASP46 |
| B | GLU119 |
| B | HOH503 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 400 |
| Chain | Residue |
| B | HIS17 |
| B | GLU44 |
| B | GLU119 |
| B | PHE152 |
| B | LEU172 |
| B | HOH504 |
| B | HOH538 |
| B | HOH607 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 401 |
| Chain | Residue |
| A | HIS17 |
| A | GLU44 |
| A | GLU119 |
| A | PHE152 |
| A | LEU172 |
| A | TRP217 |
| A | HOH503 |
| A | HOH505 |
| A | HOH521 |
| A | HOH527 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 472 |
| Details | Domain: {"description":"GP-PDE","evidences":[{"source":"PROSITE-ProRule","id":"PRU01041","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"18214974","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2PZ0","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"18214974","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2PZ0","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"18214974","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PZ0","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 8 |
| Details | M-CSA 300 |
| Chain | Residue | Details |
| A | HIS17 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ARG18 | electrostatic stabiliser, hydrogen bond donor, steric role |
| A | GLU44 | metal ligand |
| A | ASP46 | metal ligand |
| A | HIS59 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | GLU119 | metal ligand |
| A | LYS121 | electrostatic stabiliser, hydrogen bond donor |
| A | ASP239 | hydrogen bond acceptor, increase acidity, increase basicity |
| site_id | MCSA2 |
| Number of Residues | 8 |
| Details | M-CSA 300 |
| Chain | Residue | Details |
| B | HIS17 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ARG18 | electrostatic stabiliser, hydrogen bond donor, steric role |
| B | GLU44 | metal ligand |
| B | ASP46 | metal ligand |
| B | HIS59 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | GLU119 | metal ligand |
| B | LYS121 | electrostatic stabiliser, hydrogen bond donor |
| B | ASP239 | hydrogen bond acceptor, increase acidity, increase basicity |
