3OF3
Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae
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 |
A | 0042278 | biological_process | purine nucleoside metabolic process |
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 |
B | 0042278 | biological_process | purine nucleoside metabolic process |
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 |
C | 0042278 | biological_process | purine nucleoside metabolic process |
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 |
D | 0042278 | biological_process | purine nucleoside metabolic process |
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 |
E | 0042278 | biological_process | purine nucleoside metabolic process |
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 |
F | 0042278 | biological_process | purine nucleoside metabolic process |
G | 0003824 | molecular_function | catalytic activity |
G | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
G | 0005829 | cellular_component | cytosol |
G | 0006139 | biological_process | nucleobase-containing compound metabolic process |
G | 0006152 | biological_process | purine nucleoside catabolic process |
G | 0009116 | biological_process | nucleoside metabolic process |
G | 0009164 | biological_process | nucleoside catabolic process |
G | 0016757 | molecular_function | glycosyltransferase activity |
G | 0016763 | molecular_function | pentosyltransferase activity |
G | 0042278 | biological_process | purine nucleoside metabolic process |
H | 0003824 | molecular_function | catalytic activity |
H | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
H | 0005829 | cellular_component | cytosol |
H | 0006139 | biological_process | nucleobase-containing compound metabolic process |
H | 0006152 | biological_process | purine nucleoside catabolic process |
H | 0009116 | biological_process | nucleoside metabolic process |
H | 0009164 | biological_process | nucleoside catabolic process |
H | 0016757 | molecular_function | glycosyltransferase activity |
H | 0016763 | molecular_function | pentosyltransferase activity |
H | 0042278 | biological_process | purine nucleoside metabolic process |
I | 0003824 | molecular_function | catalytic activity |
I | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
I | 0005829 | cellular_component | cytosol |
I | 0006139 | biological_process | nucleobase-containing compound metabolic process |
I | 0006152 | biological_process | purine nucleoside catabolic process |
I | 0009116 | biological_process | nucleoside metabolic process |
I | 0009164 | biological_process | nucleoside catabolic process |
I | 0016757 | molecular_function | glycosyltransferase activity |
I | 0016763 | molecular_function | pentosyltransferase activity |
I | 0042278 | biological_process | purine nucleoside metabolic process |
J | 0003824 | molecular_function | catalytic activity |
J | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
J | 0005829 | cellular_component | cytosol |
J | 0006139 | biological_process | nucleobase-containing compound metabolic process |
J | 0006152 | biological_process | purine nucleoside catabolic process |
J | 0009116 | biological_process | nucleoside metabolic process |
J | 0009164 | biological_process | nucleoside catabolic process |
J | 0016757 | molecular_function | glycosyltransferase activity |
J | 0016763 | molecular_function | pentosyltransferase activity |
J | 0042278 | biological_process | purine nucleoside metabolic process |
K | 0003824 | molecular_function | catalytic activity |
K | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
K | 0005829 | cellular_component | cytosol |
K | 0006139 | biological_process | nucleobase-containing compound metabolic process |
K | 0006152 | biological_process | purine nucleoside catabolic process |
K | 0009116 | biological_process | nucleoside metabolic process |
K | 0009164 | biological_process | nucleoside catabolic process |
K | 0016757 | molecular_function | glycosyltransferase activity |
K | 0016763 | molecular_function | pentosyltransferase activity |
K | 0042278 | biological_process | purine nucleoside metabolic process |
L | 0003824 | molecular_function | catalytic activity |
L | 0004731 | molecular_function | purine-nucleoside phosphorylase activity |
L | 0005829 | cellular_component | cytosol |
L | 0006139 | biological_process | nucleobase-containing compound metabolic process |
L | 0006152 | biological_process | purine nucleoside catabolic process |
L | 0009116 | biological_process | nucleoside metabolic process |
L | 0009164 | biological_process | nucleoside catabolic process |
L | 0016757 | molecular_function | glycosyltransferase activity |
L | 0016763 | molecular_function | pentosyltransferase activity |
L | 0042278 | biological_process | purine nucleoside metabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE DIH A 500 |
Chain | Residue |
A | MET78 |
A | SER217 |
A | ASP218 |
A | PO4501 |
C | HIS18 |
C | ARG57 |
A | SER104 |
A | CYS105 |
A | GLY106 |
A | PHE173 |
A | VAL192 |
A | GLU193 |
A | MET194 |
A | GLU195 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 A 501 |
Chain | Residue |
A | GLY34 |
A | ARG38 |
A | ARG101 |
A | GLY103 |
A | SER104 |
A | DIH500 |
C | ARG57 |
site_id | AC3 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE DIH B 500 |
Chain | Residue |
B | MET78 |
B | SER104 |
B | CYS105 |
B | GLY106 |
B | PHE173 |
B | VAL192 |
B | GLU193 |
B | MET194 |
B | GLU195 |
B | SER217 |
B | ASP218 |
B | PO4501 |
B | HOH921 |
B | HOH1607 |
E | HIS18 |
E | ARG57 |
site_id | AC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 B 501 |
Chain | Residue |
B | GLY34 |
B | ARG38 |
B | ARG101 |
B | GLY103 |
B | SER104 |
B | DIH500 |
E | ARG57 |
site_id | AC5 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE DIH C 500 |
Chain | Residue |
A | HIS18 |
A | ARG57 |
C | MET78 |
C | SER104 |
C | CYS105 |
C | GLY106 |
C | PHE173 |
C | VAL192 |
C | GLU193 |
C | MET194 |
C | GLU195 |
C | SER217 |
C | ASP218 |
C | PO4501 |
C | HOH567 |
C | HOH1332 |
site_id | AC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 C 501 |
Chain | Residue |
A | ARG57 |
C | GLY34 |
C | ARG38 |
C | ARG101 |
C | GLY103 |
C | SER104 |
C | DIH500 |
site_id | AC7 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE DIH D 500 |
Chain | Residue |
D | MET78 |
D | SER104 |
D | CYS105 |
D | GLY106 |
D | PHE173 |
D | VAL192 |
D | GLU193 |
D | MET194 |
D | GLU195 |
D | SER217 |
D | ASP218 |
D | HOH419 |
D | PO4501 |
L | HIS18 |
site_id | AC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 D 501 |
Chain | Residue |
D | GLY34 |
D | ARG38 |
D | ARG101 |
D | GLY103 |
D | SER104 |
D | DIH500 |
L | ARG57 |
site_id | AC9 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE DIH E 500 |
Chain | Residue |
E | SER217 |
E | ASP218 |
E | PO4501 |
E | HOH1024 |
B | HIS18 |
B | ARG57 |
E | MET78 |
E | SER104 |
E | CYS105 |
E | GLY106 |
E | PHE173 |
E | VAL192 |
E | GLU193 |
E | MET194 |
E | GLU195 |
site_id | BC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 E 501 |
Chain | Residue |
B | ARG57 |
E | GLY34 |
E | ARG38 |
E | ARG101 |
E | GLY103 |
E | SER104 |
E | DIH500 |
site_id | BC2 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE DIH F 500 |
Chain | Residue |
F | MET78 |
F | SER104 |
F | CYS105 |
F | GLY106 |
F | PHE173 |
F | VAL192 |
F | GLU193 |
F | MET194 |
F | GLU195 |
F | SER217 |
F | ASP218 |
F | ILE220 |
F | PO4501 |
F | HOH843 |
F | HOH1347 |
J | HIS18 |
J | ARG57 |
site_id | BC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 F 501 |
Chain | Residue |
F | GLY34 |
F | ARG38 |
F | ARG101 |
F | GLY103 |
F | SER104 |
F | DIH500 |
J | ARG57 |
site_id | BC4 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE DIH G 500 |
Chain | Residue |
G | MET78 |
G | SER104 |
G | CYS105 |
G | GLY106 |
G | PHE173 |
G | VAL192 |
G | GLU193 |
G | MET194 |
G | GLU195 |
G | SER217 |
G | ASP218 |
G | PO4501 |
G | HOH1173 |
I | HIS18 |
I | ARG57 |
site_id | BC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 G 501 |
Chain | Residue |
G | GLY34 |
G | ARG38 |
G | ARG101 |
G | GLY103 |
G | SER104 |
G | DIH500 |
I | ARG57 |
site_id | BC6 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE DIH H 500 |
Chain | Residue |
H | MET78 |
H | SER104 |
H | CYS105 |
H | GLY106 |
H | PHE173 |
H | VAL192 |
H | GLU193 |
H | MET194 |
H | GLU195 |
H | SER217 |
H | ASP218 |
H | PO4501 |
H | HOH721 |
K | HIS18 |
K | ARG57 |
site_id | BC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 H 501 |
Chain | Residue |
H | GLY34 |
H | ARG38 |
H | ARG101 |
H | GLY103 |
H | SER104 |
H | DIH500 |
K | ARG57 |
site_id | BC8 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE DIH I 500 |
Chain | Residue |
G | HIS18 |
G | ARG57 |
I | MET78 |
I | SER104 |
I | CYS105 |
I | GLY106 |
I | PHE173 |
I | VAL192 |
I | GLU193 |
I | MET194 |
I | GLU195 |
I | SER217 |
I | ASP218 |
I | PO4501 |
I | HOH1091 |
site_id | BC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 I 501 |
Chain | Residue |
G | ARG57 |
I | GLY34 |
I | ARG38 |
I | ARG101 |
I | GLY103 |
I | SER104 |
I | DIH500 |
site_id | CC1 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE DIH J 500 |
Chain | Residue |
F | HIS18 |
F | ARG57 |
J | MET78 |
J | SER104 |
J | CYS105 |
J | GLY106 |
J | PHE173 |
J | VAL192 |
J | GLU193 |
J | MET194 |
J | GLU195 |
J | SER217 |
J | ASP218 |
J | PO4501 |
J | HOH791 |
site_id | CC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 J 501 |
Chain | Residue |
F | ARG57 |
J | GLY34 |
J | ARG38 |
J | ARG101 |
J | GLY103 |
J | SER104 |
J | DIH500 |
site_id | CC3 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE DIH K 500 |
Chain | Residue |
H | HIS18 |
H | ARG57 |
K | MET78 |
K | SER104 |
K | CYS105 |
K | GLY106 |
K | PHE173 |
K | VAL192 |
K | GLU193 |
K | MET194 |
K | GLU195 |
K | SER217 |
K | ASP218 |
K | PO4501 |
K | HOH561 |
K | HOH2032 |
site_id | CC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 K 501 |
Chain | Residue |
H | ARG57 |
K | GLY34 |
K | ARG38 |
K | ARG101 |
K | GLY103 |
K | SER104 |
K | DIH500 |
site_id | CC5 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE DIH L 500 |
Chain | Residue |
D | HIS18 |
D | ARG57 |
L | MET78 |
L | SER104 |
L | CYS105 |
L | GLY106 |
L | PHE173 |
L | VAL192 |
L | GLU193 |
L | GLU195 |
L | SER217 |
L | ASP218 |
L | HOH306 |
L | PO4501 |
L | HOH1213 |
L | HOH1245 |
site_id | CC6 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PO4 L 501 |
Chain | Residue |
D | ARG57 |
L | PRO33 |
L | GLY34 |
L | ARG38 |
L | ARG101 |
L | GLY103 |
L | SER104 |
L | DIH500 |
Functional Information from PROSITE/UniProt
site_id | PS01232 |
Number of Residues | 16 |
Details | PNP_UDP_1 Purine and other phosphorylases family 1 signature. GhGMGiPScSIyvtEL |
Chain | Residue | Details |
A | GLY75-LEU90 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 12 |
Details | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_01627 |
Chain | Residue | Details |
A | ASP218 | |
J | ASP218 | |
K | ASP218 | |
L | ASP218 | |
B | ASP218 | |
C | ASP218 | |
D | ASP218 | |
E | ASP218 | |
F | ASP218 | |
G | ASP218 | |
H | ASP218 | |
I | ASP218 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0007744|PDB:1VHW |
Chain | Residue | Details |
A | HIS18 | |
J | HIS18 | |
K | HIS18 | |
L | HIS18 | |
B | HIS18 | |
C | HIS18 | |
D | HIS18 | |
E | HIS18 | |
F | HIS18 | |
G | HIS18 | |
H | HIS18 | |
I | HIS18 |
site_id | SWS_FT_FI3 |
Number of Residues | 36 |
Details | BINDING: in other chain => ECO:0007744|PDB:3OF3 |
Chain | Residue | Details |
A | GLY34 | |
D | GLY34 | |
D | ARG38 | |
D | ARG101 | |
E | GLY34 | |
E | ARG38 | |
E | ARG101 | |
F | GLY34 | |
F | ARG38 | |
F | ARG101 | |
G | GLY34 | |
A | ARG38 | |
G | ARG38 | |
G | ARG101 | |
H | GLY34 | |
H | ARG38 | |
H | ARG101 | |
I | GLY34 | |
I | ARG38 | |
I | ARG101 | |
J | GLY34 | |
J | ARG38 | |
A | ARG101 | |
J | ARG101 | |
K | GLY34 | |
K | ARG38 | |
K | ARG101 | |
L | GLY34 | |
L | ARG38 | |
L | ARG101 | |
B | GLY34 | |
B | ARG38 | |
B | ARG101 | |
C | GLY34 | |
C | ARG38 | |
C | ARG101 |
site_id | SWS_FT_FI4 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0007744|PDB:3OF3 |
Chain | Residue | Details |
A | ARG57 | |
J | ARG57 | |
K | ARG57 | |
L | ARG57 | |
B | ARG57 | |
C | ARG57 | |
D | ARG57 | |
E | ARG57 | |
F | ARG57 | |
G | ARG57 | |
H | ARG57 | |
I | ARG57 |
site_id | SWS_FT_FI5 |
Number of Residues | 12 |
Details | BINDING: in other chain => ECO:0007744|PDB:1VHW |
Chain | Residue | Details |
A | GLU193 | |
J | GLU193 | |
K | GLU193 | |
L | GLU193 | |
B | GLU193 | |
C | GLU193 | |
D | GLU193 | |
E | GLU193 | |
F | GLU193 | |
G | GLU193 | |
H | GLU193 | |
I | GLU193 |
site_id | SWS_FT_FI6 |
Number of Residues | 12 |
Details | BINDING: in other chain => ECO:0000250|UniProtKB:P50389 |
Chain | Residue | Details |
A | SER217 | |
J | SER217 | |
K | SER217 | |
L | SER217 | |
B | SER217 | |
C | SER217 | |
D | SER217 | |
E | SER217 | |
F | SER217 | |
G | SER217 | |
H | SER217 | |
I | SER217 |
site_id | SWS_FT_FI7 |
Number of Residues | 12 |
Details | SITE: Important for catalytic activity => ECO:0000255|HAMAP-Rule:MF_01627 |
Chain | Residue | Details |
A | ARG231 | |
J | ARG231 | |
K | ARG231 | |
L | ARG231 | |
B | ARG231 | |
C | ARG231 | |
D | ARG231 | |
E | ARG231 | |
F | ARG231 | |
G | ARG231 | |
H | ARG231 | |
I | ARG231 |