Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

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
D	HIS4
D	ARG43
E	HIS4
E	ARG43
F	HIS4
F	ARG43
C	ARG43
A	HIS4
A	ARG43
B	HIS4
B	ARG43
C	HIS4

site_id	SWS_FT_FI3
Number of Residues	30
Details	BINDING: in other chain => ECO:0000250\|UniProtKB:P50389

Chain	Residue	Details
B	ARG24
B	ARG87
B	GLU179
B	SER203
C	GLY20
C	ARG24
C	ARG87
C	GLU179
C	SER203
D	GLY20
D	ARG24
D	ARG87
D	GLU179
D	SER203
E	GLY20
E	ARG24
E	ARG87
E	GLU179
E	SER203
F	GLY20
F	ARG24
F	ARG87
F	GLU179
F	SER203
A	GLY20
A	ARG24
A	ARG87
A	GLU179
A	SER203
B	GLY20

site_id	SWS_FT_FI4
Number of Residues	6
Details	SITE: Important for catalytic activity => ECO:0000255\|HAMAP-Rule:MF_01627

Chain	Residue	Details
C	ARG217
D	ARG217
E	ARG217
F	ARG217
A	ARG217
B	ARG217

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