Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

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
B	ASP218
C	ASP218
D	ASP218
E	ASP218
F	ASP218
G	ASP218
H	ASP218
I	ASP218
J	ASP218
K	ASP218
L	ASP218

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0007744\|PDB:1VHW

Chain	Residue	Details
A	HIS18
B	HIS18
D	HIS18
E	HIS18
F	HIS18
G	HIS18
H	HIS18
I	HIS18
J	HIS18
K	HIS18
L	HIS18
C	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	ARG38
D	ARG101
E	GLY34
E	ARG38
E	ARG101
F	GLY34
F	ARG38
F	ARG101
G	GLY34
G	ARG38
G	ARG101
H	GLY34
H	ARG38
H	ARG101
I	GLY34
I	ARG38
I	ARG101
J	GLY34
J	ARG38
J	ARG101
K	GLY34
K	ARG38
K	ARG101
L	GLY34
L	ARG38
L	ARG101
A	ARG38
A	ARG101
B	GLY34
B	ARG38
B	ARG101
C	GLY34
C	ARG38
C	ARG101
D	GLY34

site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0007744\|PDB:3OF3

Chain	Residue	Details
K	ARG57
A	ARG57
B	ARG57
C	ARG57
D	ARG57
E	ARG57
F	ARG57
G	ARG57
H	ARG57
I	ARG57
J	ARG57
L	ARG57

site_id	SWS_FT_FI5
Number of Residues	12
Details	BINDING: in other chain => ECO:0007744\|PDB:1VHW

Chain	Residue	Details
A	GLU193
B	GLU193
C	GLU193
D	GLU193
E	GLU193
F	GLU193
G	GLU193
H	GLU193
I	GLU193
J	GLU193
K	GLU193
L	GLU193

site_id	SWS_FT_FI6
Number of Residues	12
Details	BINDING: in other chain => ECO:0000250\|UniProtKB:P50389

Chain	Residue	Details
A	SER217
B	SER217
C	SER217
D	SER217
E	SER217
F	SER217
G	SER217
H	SER217
I	SER217
J	SER217
K	SER217
L	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
B	ARG231
C	ARG231
D	ARG231
E	ARG231
F	ARG231
G	ARG231
H	ARG231
I	ARG231
J	ARG231
K	ARG231
L	ARG231

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)