2F9R
Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005576 | cellular_component | extracellular region |
| A | 0006629 | biological_process | lipid metabolic process |
| A | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| A | 0016042 | biological_process | lipid catabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0031640 | biological_process | killing of cells of another organism |
| A | 0035821 | biological_process | modulation of process of another organism |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0090729 | molecular_function | toxin activity |
| B | 0005576 | cellular_component | extracellular region |
| B | 0006629 | biological_process | lipid metabolic process |
| B | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| B | 0016042 | biological_process | lipid catabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0031640 | biological_process | killing of cells of another organism |
| B | 0035821 | biological_process | modulation of process of another organism |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0090729 | molecular_function | toxin activity |
| C | 0005576 | cellular_component | extracellular region |
| C | 0006629 | biological_process | lipid metabolic process |
| C | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| C | 0016042 | biological_process | lipid catabolic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0031640 | biological_process | killing of cells of another organism |
| C | 0035821 | biological_process | modulation of process of another organism |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0090729 | molecular_function | toxin activity |
| D | 0005576 | cellular_component | extracellular region |
| D | 0006629 | biological_process | lipid metabolic process |
| D | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| D | 0016042 | biological_process | lipid catabolic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0031640 | biological_process | killing of cells of another organism |
| D | 0035821 | biological_process | modulation of process of another organism |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0090729 | molecular_function | toxin activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 601 |
| Chain | Residue |
| A | GLU32 |
| A | ASP34 |
| A | ASP91 |
| A | TRP230 |
| A | HOH719 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 602 |
| Chain | Residue |
| B | HOH734 |
| B | GLU32 |
| B | ASP34 |
| B | ASP91 |
| B | HOH733 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG C 603 |
| Chain | Residue |
| C | GLU32 |
| C | ASP34 |
| C | ASP91 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 604 |
| Chain | Residue |
| D | GLU32 |
| D | ASP34 |
| D | ASP91 |
| D | TRP230 |
| D | HOH767 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EPE B 701 |
| Chain | Residue |
| B | ALA16 |
| B | ARG59 |
| B | TRP60 |
| B | GLU61 |
| B | TYR62 |
| B | VAL65 |
| B | HOH726 |
| B | HOH741 |
| B | HOH794 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EPE C 703 |
| Chain | Residue |
| B | ARG4 |
| B | ASN267 |
| C | ALA16 |
| C | ARG59 |
| C | TRP60 |
| C | GLU61 |
| C | VAL65 |
| C | HOH751 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EPE D 704 |
| Chain | Residue |
| A | ARG4 |
| A | ASN267 |
| D | ALA16 |
| D | ARG59 |
| D | TRP60 |
| D | GLU61 |
| D | HOH758 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15654080 |
| Chain | Residue | Details |
| A | HIS12 | |
| B | HIS12 | |
| C | HIS12 | |
| D | HIS12 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:15654080 |
| Chain | Residue | Details |
| A | HIS47 | |
| B | HIS47 | |
| C | HIS47 | |
| D | HIS47 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15654080, ECO:0000269|PubMed:16480957, ECO:0000312|PDB:1XX1, ECO:0000312|PDB:2F9R |
| Chain | Residue | Details |
| A | GLU32 | |
| D | GLU32 | |
| D | ASP34 | |
| D | ASP91 | |
| A | ASP34 | |
| A | ASP91 | |
| B | GLU32 | |
| B | ASP34 | |
| B | ASP91 | |
| C | GLU32 | |
| C | ASP34 | |
| C | ASP91 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 9 |
| Details | a catalytic site defined by CSA, PubMed 15654080 |
| Chain | Residue | Details |
| A | ASP34 | |
| A | ASP233 | |
| A | HIS12 | |
| A | TRP230 | |
| A | GLY48 | |
| A | HIS47 | |
| A | ASP52 | |
| A | LYS93 | |
| A | ASN252 |
| site_id | CSA2 |
| Number of Residues | 9 |
| Details | a catalytic site defined by CSA, PubMed 15654080 |
| Chain | Residue | Details |
| B | ASP34 | |
| B | ASP233 | |
| B | HIS12 | |
| B | TRP230 | |
| B | GLY48 | |
| B | HIS47 | |
| B | ASP52 | |
| B | LYS93 | |
| B | ASN252 |
| site_id | CSA3 |
| Number of Residues | 9 |
| Details | a catalytic site defined by CSA, PubMed 15654080 |
| Chain | Residue | Details |
| C | ASP34 | |
| C | ASP233 | |
| C | HIS12 | |
| C | TRP230 | |
| C | GLY48 | |
| C | HIS47 | |
| C | ASP52 | |
| C | LYS93 | |
| C | ASN252 |
| site_id | CSA4 |
| Number of Residues | 9 |
| Details | a catalytic site defined by CSA, PubMed 15654080 |
| Chain | Residue | Details |
| D | ASP34 | |
| D | ASP233 | |
| D | HIS12 | |
| D | TRP230 | |
| D | GLY48 | |
| D | HIS47 | |
| D | ASP52 | |
| D | LYS93 | |
| D | ASN252 |
| site_id | MCSA1 |
| Number of Residues | 11 |
| Details | M-CSA 242 |
| Chain | Residue | Details |
| A | HIS12 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ASP233 | activator, hydrogen bond acceptor |
| A | ASN252 | activator, hydrogen bond acceptor, hydrogen bond donor |
| A | GLU32 | metal ligand |
| A | ASP34 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand |
| A | HIS47 | covalently attached, hydrogen bond donor, nucleofuge, nucleophile |
| A | GLY48 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| A | ASP52 | activator, hydrogen bond acceptor |
| A | ASP91 | metal ligand |
| A | LYS93 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor |
| A | TRP230 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 11 |
| Details | M-CSA 242 |
| Chain | Residue | Details |
| B | HIS12 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ASP233 | activator, hydrogen bond acceptor |
| B | ASN252 | activator, hydrogen bond acceptor, hydrogen bond donor |
| B | GLU32 | metal ligand |
| B | ASP34 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand |
| B | HIS47 | covalently attached, hydrogen bond donor, nucleofuge, nucleophile |
| B | GLY48 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| B | ASP52 | activator, hydrogen bond acceptor |
| B | ASP91 | metal ligand |
| B | LYS93 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor |
| B | TRP230 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 11 |
| Details | M-CSA 242 |
| Chain | Residue | Details |
| C | HIS12 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | ASP233 | activator, hydrogen bond acceptor |
| C | ASN252 | activator, hydrogen bond acceptor, hydrogen bond donor |
| C | GLU32 | metal ligand |
| C | ASP34 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand |
| C | HIS47 | covalently attached, hydrogen bond donor, nucleofuge, nucleophile |
| C | GLY48 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| C | ASP52 | activator, hydrogen bond acceptor |
| C | ASP91 | metal ligand |
| C | LYS93 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor |
| C | TRP230 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 11 |
| Details | M-CSA 242 |
| Chain | Residue | Details |
| D | HIS12 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| D | ASP233 | activator, hydrogen bond acceptor |
| D | ASN252 | activator, hydrogen bond acceptor, hydrogen bond donor |
| D | GLU32 | metal ligand |
| D | ASP34 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand |
| D | HIS47 | covalently attached, hydrogen bond donor, nucleofuge, nucleophile |
| D | GLY48 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| D | ASP52 | activator, hydrogen bond acceptor |
| D | ASP91 | metal ligand |
| D | LYS93 | attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor |
| D | TRP230 | electrostatic stabiliser, hydrogen bond donor |
