6DZ2
Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004645 | molecular_function | 1,4-alpha-oligoglucan phosphorylase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| A | 0006166 | biological_process | purine ribonucleoside salvage |
| A | 0006738 | biological_process | nicotinamide riboside catabolic process |
| A | 0009116 | biological_process | nucleoside metabolic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016757 | molecular_function | glycosyltransferase activity |
| A | 0016763 | molecular_function | pentosyltransferase activity |
| A | 0017061 | molecular_function | S-methyl-5-thioadenosine phosphorylase activity |
| A | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004645 | molecular_function | 1,4-alpha-oligoglucan phosphorylase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| B | 0006166 | biological_process | purine ribonucleoside salvage |
| B | 0006738 | biological_process | nicotinamide riboside catabolic process |
| B | 0009116 | biological_process | nucleoside metabolic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016757 | molecular_function | glycosyltransferase activity |
| B | 0016763 | molecular_function | pentosyltransferase activity |
| B | 0017061 | molecular_function | S-methyl-5-thioadenosine phosphorylase activity |
| B | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004645 | molecular_function | 1,4-alpha-oligoglucan phosphorylase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| C | 0006166 | biological_process | purine ribonucleoside salvage |
| C | 0006738 | biological_process | nicotinamide riboside catabolic process |
| C | 0009116 | biological_process | nucleoside metabolic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016757 | molecular_function | glycosyltransferase activity |
| C | 0016763 | molecular_function | pentosyltransferase activity |
| C | 0017061 | molecular_function | S-methyl-5-thioadenosine phosphorylase activity |
| C | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| C | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 301 |
| Chain | Residue |
| A | LEU280 |
| A | HOH493 |
| B | EDO301 |
| C | EDO302 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 303 |
| Chain | Residue |
| A | LYS241 |
| B | HOH476 |
| C | EDO303 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue CL A 304 |
| Chain | Residue |
| B | ARG116 |
| C | ARG116 |
| A | ARG116 |
| A | HOH494 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue CL A 305 |
| Chain | Residue |
| A | THR93 |
| A | ASN195 |
| A | MET196 |
| A | THR197 |
| A | OS5307 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue ACY A 306 |
| Chain | Residue |
| A | THR118 |
| A | MET119 |
| B | MET119 |
| C | THR118 |
| C | MET119 |
| site_id | AC6 |
| Number of Residues | 19 |
| Details | binding site for residue OS5 A 307 |
| Chain | Residue |
| A | GLY16 |
| A | THR18 |
| A | THR92 |
| A | ALA94 |
| A | CYS95 |
| A | GLY96 |
| A | PHE177 |
| A | ILE194 |
| A | ASN195 |
| A | THR219 |
| A | ASP220 |
| A | ASP222 |
| A | VAL236 |
| A | LEU240 |
| A | CL305 |
| A | HOH420 |
| A | HOH473 |
| C | HIS137 |
| C | LEU279 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 301 |
| Chain | Residue |
| A | PHE276 |
| A | EDO301 |
| B | ASP234 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue CL B 302 |
| Chain | Residue |
| B | THR93 |
| B | ASN195 |
| B | MET196 |
| B | THR197 |
| B | OS5303 |
| site_id | AC9 |
| Number of Residues | 20 |
| Details | binding site for residue OS5 B 303 |
| Chain | Residue |
| A | HIS137 |
| A | LEU279 |
| B | GLY16 |
| B | THR18 |
| B | PRO69 |
| B | ALA94 |
| B | CYS95 |
| B | GLY96 |
| B | PHE177 |
| B | ILE194 |
| B | ASN195 |
| B | MET196 |
| B | THR219 |
| B | ASP220 |
| B | ASP222 |
| B | LEU240 |
| B | ALA244 |
| B | CL302 |
| B | HOH406 |
| B | HOH418 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 301 |
| Chain | Residue |
| C | THR261 |
| C | GLU262 |
| C | EDO302 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 302 |
| Chain | Residue |
| A | EDO301 |
| B | LYS241 |
| C | EDO301 |
| C | EDO304 |
| C | EDO306 |
| C | HOH464 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 303 |
| Chain | Residue |
| A | EDO303 |
| C | LEU280 |
| C | EDO305 |
| site_id | AD4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 304 |
| Chain | Residue |
| C | EDO302 |
| C | EDO306 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 305 |
| Chain | Residue |
| A | ASP234 |
| C | PHE276 |
| C | VAL278 |
| C | EDO303 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 306 |
| Chain | Residue |
| C | EDO302 |
| C | EDO304 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue CL C 307 |
| Chain | Residue |
| C | THR93 |
| C | ASN195 |
| C | MET196 |
| C | THR197 |
| C | OS5308 |
| site_id | AD8 |
| Number of Residues | 17 |
| Details | binding site for residue OS5 C 308 |
| Chain | Residue |
| C | GLY96 |
| C | PHE177 |
| C | ILE194 |
| C | ASN195 |
| C | THR219 |
| C | ASP220 |
| C | ASP222 |
| C | LEU240 |
| C | ALA244 |
| C | CL307 |
| C | HOH417 |
| B | HIS137 |
| B | LEU279 |
| C | THR18 |
| C | THR93 |
| C | ALA94 |
| C | CYS95 |
Functional Information from PROSITE/UniProt
| site_id | PS01240 |
| Number of Residues | 41 |
| Details | PNP_MTAP_2 Purine and other phosphorylases family 2 signature. LarhGrqHtImpskVnyqAn.IwAlkeeGcth.VIvtTAcGSL |
| Chain | Residue | Details |
| A | LEU58-LEU98 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 20 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | Site: {"description":"Important for substrate specificity"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9CQ65","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 244 |
| Chain | Residue | Details |
| A | ASP220 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ASP222 | electrostatic stabiliser |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 244 |
| Chain | Residue | Details |
| B | ASP220 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ASP222 | electrostatic stabiliser |
| site_id | MCSA3 |
| Number of Residues | 2 |
| Details | M-CSA 244 |
| Chain | Residue | Details |
| C | ASP220 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | ASP222 | electrostatic stabiliser |
