6F4X
Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin A
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
A | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
A | 0005829 | cellular_component | cytosol |
A | 0006139 | biological_process | nucleobase-containing compound metabolic process |
A | 0006152 | biological_process | purine nucleoside catabolic process |
A | 0009116 | biological_process | nucleoside metabolic process |
A | 0009164 | biological_process | nucleoside catabolic process |
A | 0016757 | molecular_function | glycosyltransferase activity |
A | 0016763 | molecular_function | pentosyltransferase activity |
B | 0003824 | molecular_function | catalytic activity |
B | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
B | 0005829 | cellular_component | cytosol |
B | 0006139 | biological_process | nucleobase-containing compound metabolic process |
B | 0006152 | biological_process | purine nucleoside catabolic process |
B | 0009116 | biological_process | nucleoside metabolic process |
B | 0009164 | biological_process | nucleoside catabolic process |
B | 0016757 | molecular_function | glycosyltransferase activity |
B | 0016763 | molecular_function | pentosyltransferase activity |
C | 0003824 | molecular_function | catalytic activity |
C | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
C | 0005829 | cellular_component | cytosol |
C | 0006139 | biological_process | nucleobase-containing compound metabolic process |
C | 0006152 | biological_process | purine nucleoside catabolic process |
C | 0009116 | biological_process | nucleoside metabolic process |
C | 0009164 | biological_process | nucleoside catabolic process |
C | 0016757 | molecular_function | glycosyltransferase activity |
C | 0016763 | molecular_function | pentosyltransferase activity |
D | 0003824 | molecular_function | catalytic activity |
D | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
D | 0005829 | cellular_component | cytosol |
D | 0006139 | biological_process | nucleobase-containing compound metabolic process |
D | 0006152 | biological_process | purine nucleoside catabolic process |
D | 0009116 | biological_process | nucleoside metabolic process |
D | 0009164 | biological_process | nucleoside catabolic process |
D | 0016757 | molecular_function | glycosyltransferase activity |
D | 0016763 | molecular_function | pentosyltransferase activity |
E | 0003824 | molecular_function | catalytic activity |
E | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
E | 0005829 | cellular_component | cytosol |
E | 0006139 | biological_process | nucleobase-containing compound metabolic process |
E | 0006152 | biological_process | purine nucleoside catabolic process |
E | 0009116 | biological_process | nucleoside metabolic process |
E | 0009164 | biological_process | nucleoside catabolic process |
E | 0016757 | molecular_function | glycosyltransferase activity |
E | 0016763 | molecular_function | pentosyltransferase activity |
F | 0003824 | molecular_function | catalytic activity |
F | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
F | 0005829 | cellular_component | cytosol |
F | 0006139 | biological_process | nucleobase-containing compound metabolic process |
F | 0006152 | biological_process | purine nucleoside catabolic process |
F | 0009116 | biological_process | nucleoside metabolic process |
F | 0009164 | biological_process | nucleoside catabolic process |
F | 0016757 | molecular_function | glycosyltransferase activity |
F | 0016763 | molecular_function | pentosyltransferase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 14 |
Details | binding site for residue FMC A 301 |
Chain | Residue |
A | ARG87 |
A | LEU206 |
A | PO4302 |
A | HOH536 |
D | HIS4 |
D | ARG43 |
A | THR90 |
A | CYS91 |
A | GLY92 |
A | PHE159 |
A | GLU179 |
A | MET180 |
A | GLU181 |
A | SER203 |
site_id | AC2 |
Number of Residues | 8 |
Details | binding site for residue PO4 A 302 |
Chain | Residue |
A | GLY20 |
A | ASP21 |
A | ARG87 |
A | GLY89 |
A | THR90 |
A | FMC301 |
A | HOH464 |
D | ARG43 |
site_id | AC3 |
Number of Residues | 6 |
Details | binding site for residue EDO A 303 |
Chain | Residue |
A | TYR13 |
A | ASP35 |
A | LYS37 |
A | SER49 |
A | GLY50 |
A | LYS51 |
site_id | AC4 |
Number of Residues | 4 |
Details | binding site for residue EDO A 304 |
Chain | Residue |
A | LYS78 |
A | GLU191 |
D | PHE162 |
D | HOH494 |
site_id | AC5 |
Number of Residues | 2 |
Details | binding site for residue EDO A 305 |
Chain | Residue |
A | GLU38 |
A | ASN41 |
site_id | AC6 |
Number of Residues | 5 |
Details | binding site for residue EDO A 306 |
Chain | Residue |
A | LYS30 |
A | ALA36 |
A | PHE48 |
A | HOH511 |
D | ILE226 |
site_id | AC7 |
Number of Residues | 5 |
Details | binding site for residue EDO A 307 |
Chain | Residue |
A | ARG117 |
A | VAL118 |
A | ASN122 |
A | HOH538 |
D | GLU163 |
site_id | AC8 |
Number of Residues | 16 |
Details | binding site for residue FMC B 301 |
Chain | Residue |
B | MET64 |
B | ARG87 |
B | THR90 |
B | CYS91 |
B | GLY92 |
B | PHE159 |
B | GLU179 |
B | MET180 |
B | GLU181 |
B | ASP204 |
B | LEU206 |
B | HOH431 |
B | HOH502 |
E | HIS4 |
E | ARG43 |
E | HOH482 |
site_id | AC9 |
Number of Residues | 3 |
Details | binding site for residue EDO B 302 |
Chain | Residue |
B | GLN15 |
B | ARG55 |
B | LYS83 |
site_id | AD1 |
Number of Residues | 8 |
Details | binding site for residue PO4 C 301 |
Chain | Residue |
C | CYS19 |
C | GLY20 |
C | ARG24 |
C | ARG87 |
C | GLY89 |
C | THR90 |
C | FMC302 |
F | ARG43 |
site_id | AD2 |
Number of Residues | 15 |
Details | binding site for residue FMC C 302 |
Chain | Residue |
C | MET64 |
C | ARG87 |
C | THR90 |
C | CYS91 |
C | GLY92 |
C | PHE159 |
C | GLU179 |
C | MET180 |
C | GLU181 |
C | SER203 |
C | ASP204 |
C | PO4301 |
C | HOH445 |
F | HIS4 |
F | ARG43 |
site_id | AD3 |
Number of Residues | 4 |
Details | binding site for residue EDO C 303 |
Chain | Residue |
C | LYS78 |
C | GLU191 |
F | PHE162 |
F | HOH473 |
site_id | AD4 |
Number of Residues | 18 |
Details | binding site for residue FMC D 301 |
Chain | Residue |
D | MET180 |
D | GLU181 |
D | SER203 |
D | LEU206 |
D | HOH427 |
D | HOH441 |
D | HOH464 |
D | HOH509 |
D | HOH510 |
A | HIS4 |
A | ARG43 |
D | MET64 |
D | ARG87 |
D | THR90 |
D | CYS91 |
D | GLY92 |
D | PHE159 |
D | GLU179 |
site_id | AD5 |
Number of Residues | 4 |
Details | binding site for residue EDO D 302 |
Chain | Residue |
D | CYS19 |
D | ARG24 |
D | THR90 |
D | PHE221 |
site_id | AD6 |
Number of Residues | 4 |
Details | binding site for residue EDO D 303 |
Chain | Residue |
B | VAL150 |
D | ASP130 |
D | PHE131 |
D | GLU132 |
site_id | AD7 |
Number of Residues | 4 |
Details | binding site for residue EDO D 304 |
Chain | Residue |
A | GLU216 |
D | PRO96 |
D | LYS97 |
D | HOH407 |
site_id | AD8 |
Number of Residues | 9 |
Details | binding site for residue PO4 E 301 |
Chain | Residue |
B | ARG43 |
E | CYS19 |
E | GLY20 |
E | ASP21 |
E | ARG24 |
E | ARG87 |
E | GLY89 |
E | THR90 |
E | FMC302 |
site_id | AD9 |
Number of Residues | 19 |
Details | binding site for residue FMC E 302 |
Chain | Residue |
B | HIS4 |
B | ARG43 |
E | MET64 |
E | ARG87 |
E | THR90 |
E | CYS91 |
E | GLY92 |
E | PHE159 |
E | ILE178 |
E | GLU179 |
E | MET180 |
E | GLU181 |
E | SER203 |
E | ASP204 |
E | LEU206 |
E | PO4301 |
E | HOH463 |
E | HOH474 |
E | HOH481 |
site_id | AE1 |
Number of Residues | 7 |
Details | binding site for residue EDO E 303 |
Chain | Residue |
C | ARG119 |
E | LEU169 |
E | LYS172 |
E | TYR173 |
E | HOH403 |
E | HOH525 |
F | PHE162 |
site_id | AE2 |
Number of Residues | 16 |
Details | binding site for residue FMC F 301 |
Chain | Residue |
C | HIS4 |
C | ARG43 |
F | MET64 |
F | ARG87 |
F | THR90 |
F | CYS91 |
F | GLY92 |
F | PHE159 |
F | GLU179 |
F | MET180 |
F | GLU181 |
F | SER203 |
F | ASP204 |
F | LEU206 |
F | HOH407 |
F | HOH466 |
site_id | AE3 |
Number of Residues | 5 |
Details | binding site for residue EDO F 302 |
Chain | Residue |
F | GLY10 |
F | ASP11 |
F | TYR13 |
F | SER49 |
F | HOH413 |
Functional Information from PROSITE/UniProt
site_id | PS01232 |
Number of Residues | 16 |
Details | PNP_UDP_1 Purine and other phosphorylases family 1 signature. GhGMGiAScTIyvtEL |
Chain | Residue | Details |
A | GLY61-LEU76 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_01627 |
Chain | Residue | Details |
A | ASP204 | |
B | ASP204 | |
C | ASP204 | |
D | ASP204 | |
E | ASP204 | |
F | ASP204 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000250|UniProtKB:P50389 |
Chain | Residue | Details |
A | HIS4 | |
E | ARG43 | |
F | HIS4 | |
F | ARG43 | |
A | ARG43 | |
B | HIS4 | |
B | ARG43 | |
C | HIS4 | |
C | ARG43 | |
D | HIS4 | |
D | ARG43 | |
E | HIS4 |
site_id | SWS_FT_FI3 |
Number of Residues | 30 |
Details | BINDING: in other chain => ECO:0000250|UniProtKB:P50389 |
Chain | Residue | Details |
A | GLY20 | |
B | SER203 | |
C | GLY20 | |
C | ARG24 | |
C | ARG87 | |
C | GLU179 | |
C | SER203 | |
D | GLY20 | |
D | ARG24 | |
D | ARG87 | |
D | GLU179 | |
A | ARG24 | |
D | SER203 | |
E | GLY20 | |
E | ARG24 | |
E | ARG87 | |
E | GLU179 | |
E | SER203 | |
F | GLY20 | |
F | ARG24 | |
F | ARG87 | |
F | GLU179 | |
A | ARG87 | |
F | SER203 | |
A | GLU179 | |
A | SER203 | |
B | GLY20 | |
B | ARG24 | |
B | ARG87 | |
B | GLU179 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | SITE: Important for catalytic activity => ECO:0000255|HAMAP-Rule:MF_01627 |
Chain | Residue | Details |
A | ARG217 | |
B | ARG217 | |
C | ARG217 | |
D | ARG217 | |
E | ARG217 | |
F | ARG217 |