Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LOK

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004850	molecular_function	uridine phosphorylase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0009116	biological_process	nucleoside metabolic process
A	0009164	biological_process	nucleoside catabolic process
A	0009166	biological_process	nucleotide catabolic process
A	0016757	molecular_function	glycosyltransferase activity
A	0016763	molecular_function	pentosyltransferase activity
A	0044206	biological_process	UMP salvage
A	0046872	molecular_function	metal ion binding
A	0047847	molecular_function	deoxyuridine phosphorylase activity
B	0003824	molecular_function	catalytic activity
B	0004850	molecular_function	uridine phosphorylase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0009116	biological_process	nucleoside metabolic process
B	0009164	biological_process	nucleoside catabolic process
B	0009166	biological_process	nucleotide catabolic process
B	0016757	molecular_function	glycosyltransferase activity
B	0016763	molecular_function	pentosyltransferase activity
B	0044206	biological_process	UMP salvage
B	0046872	molecular_function	metal ion binding
B	0047847	molecular_function	deoxyuridine phosphorylase activity
C	0003824	molecular_function	catalytic activity
C	0004850	molecular_function	uridine phosphorylase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0009116	biological_process	nucleoside metabolic process
C	0009164	biological_process	nucleoside catabolic process
C	0009166	biological_process	nucleotide catabolic process
C	0016757	molecular_function	glycosyltransferase activity
C	0016763	molecular_function	pentosyltransferase activity
C	0044206	biological_process	UMP salvage
C	0046872	molecular_function	metal ion binding
C	0047847	molecular_function	deoxyuridine phosphorylase activity
D	0003824	molecular_function	catalytic activity
D	0004850	molecular_function	uridine phosphorylase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0009116	biological_process	nucleoside metabolic process
D	0009164	biological_process	nucleoside catabolic process
D	0009166	biological_process	nucleotide catabolic process
D	0016757	molecular_function	glycosyltransferase activity
D	0016763	molecular_function	pentosyltransferase activity
D	0044206	biological_process	UMP salvage
D	0046872	molecular_function	metal ion binding
D	0047847	molecular_function	deoxyuridine phosphorylase activity
E	0003824	molecular_function	catalytic activity
E	0004850	molecular_function	uridine phosphorylase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0009116	biological_process	nucleoside metabolic process
E	0009164	biological_process	nucleoside catabolic process
E	0009166	biological_process	nucleotide catabolic process
E	0016757	molecular_function	glycosyltransferase activity
E	0016763	molecular_function	pentosyltransferase activity
E	0044206	biological_process	UMP salvage
E	0046872	molecular_function	metal ion binding
E	0047847	molecular_function	deoxyuridine phosphorylase activity
F	0003824	molecular_function	catalytic activity
F	0004850	molecular_function	uridine phosphorylase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0009116	biological_process	nucleoside metabolic process
F	0009164	biological_process	nucleoside catabolic process
F	0009166	biological_process	nucleotide catabolic process
F	0016757	molecular_function	glycosyltransferase activity
F	0016763	molecular_function	pentosyltransferase activity
F	0044206	biological_process	UMP salvage
F	0046872	molecular_function	metal ion binding
F	0047847	molecular_function	deoxyuridine phosphorylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	binding site for residue EDO A 301

Chain	Residue
A	ARG178
A	HOH433
A	HOH484
A	HOH489
A	HOH535
A	HOH615
B	LEU120
F	HOH405

site_id	AC2
Number of Residues	6
Details	binding site for residue K A 302

Chain	Residue
A	ILE68
A	SER72
B	GLU48
B	ILE68
B	SER72
A	GLU48

site_id	AC3
Number of Residues	20
Details	binding site for residue CTN A 303

Chain	Residue
A	THR93
A	THR94
A	GLY95
A	PHE161
A	GLN165
A	ARG167
A	PHE194
A	GLU195
A	MET196
A	GLU197
A	ILE220
A	CYT304
A	GOL305
A	SO4306
A	HOH402
A	HOH409
A	HOH419
A	HOH442
A	HOH450
B	HIS7

site_id	AC4
Number of Residues	12
Details	binding site for residue CYT A 304

Chain	Residue
A	THR93
A	THR94
A	GLY95
A	PHE161
A	GLN165
A	ARG167
A	GLU195
A	MET196
A	ILE220
A	CTN303
A	GOL305
A	HOH442

site_id	AC5
Number of Residues	10
Details	binding site for residue GOL A 305

Chain	Residue
A	ILE68
A	THR93
A	GLU197
A	CTN303
A	CYT304
A	SO4306
A	HOH409
A	HOH419
A	HOH450
B	HIS7

site_id	AC6
Number of Residues	15
Details	binding site for residue SO4 A 306

Chain	Residue
A	PRO24
A	GLY25
A	ASP26
A	ARG29
A	ARG90
A	VAL91
A	GLY92
A	THR93
A	GLU237
A	CTN303
A	GOL305
A	HOH402
A	HOH409
A	HOH419
B	ARG47

site_id	AC7
Number of Residues	4
Details	binding site for residue CL B 301

Chain	Residue
B	GLY25
B	ASP26
B	HOH431
B	HOH610

site_id	AC8
Number of Residues	3
Details	binding site for residue CL B 302

Chain	Residue
B	ILE220
B	ASN221
B	HOH541

site_id	AC9
Number of Residues	7
Details	binding site for residue EDO B 303

Chain	Residue
A	LEU120
B	ARG178
B	HOH432
B	HOH490
B	HOH494
B	HOH507
B	HOH574

site_id	AD1
Number of Residues	17
Details	binding site for residue CTN B 304

Chain	Residue
B	HOH415
B	HOH491
B	HOH510
A	HIS7
B	THR93
B	THR94
B	GLY95
B	PHE161
B	GLN165
B	PHE194
B	GLU195
B	MET196
B	GLU197
B	ILE220
B	CYT305
B	GOL306
B	HOH403

site_id	AD2
Number of Residues	11
Details	binding site for residue CYT B 305

Chain	Residue
B	THR94
B	GLY95
B	PHE161
B	GLN165
B	ARG167
B	GLU195
B	MET196
B	ILE220
B	CTN304
B	GOL306
B	HOH491

site_id	AD3
Number of Residues	8
Details	binding site for residue GOL B 306

Chain	Residue
A	HIS7
B	ILE68
B	THR93
B	GLU197
B	CTN304
B	CYT305
B	HOH415
B	HOH510

site_id	AD4
Number of Residues	3
Details	binding site for residue CL C 301

Chain	Residue
C	GLY25
C	ASP26
C	ARG29

site_id	AD5
Number of Residues	6
Details	binding site for residue K C 302

Chain	Residue
C	GLU48
C	ILE68
C	SER72
D	GLU48
D	ILE68
D	SER72

site_id	AD6
Number of Residues	18
Details	binding site for residue CTN C 303

Chain	Residue
C	THR93
C	THR94
C	GLY95
C	PHE161
C	GLN165
C	ARG167
C	GLU195
C	MET196
C	GLU197
C	ILE220
C	CYT304
C	GOL305
C	HOH410
C	HOH440
C	HOH491
C	HOH504
C	HOH535
D	HIS7

site_id	AD7
Number of Residues	12
Details	binding site for residue CYT C 304

Chain	Residue
C	THR94
C	GLY95
C	PHE161
C	GLN165
C	ARG167
C	PHE194
C	GLU195
C	MET196
C	ILE220
C	CTN303
C	GOL305
C	HOH504

site_id	AD8
Number of Residues	9
Details	binding site for residue GOL C 305

Chain	Residue
C	ILE68
C	THR93
C	GLU197
C	CTN303
C	CYT304
C	HOH410
C	HOH440
C	HOH491
D	HIS7

site_id	AD9
Number of Residues	6
Details	binding site for residue CYT D 301

Chain	Residue
A	GLN224
A	ASP229
D	TYR168
D	HOH401
D	HOH411
D	HOH464

site_id	AE1
Number of Residues	17
Details	binding site for residue CTN D 302

Chain	Residue
C	HIS7
D	THR93
D	THR94
D	GLY95
D	PHE161
D	GLN165
D	ARG167
D	GLU195
D	MET196
D	GLU197
D	ILE220
D	CYT303
D	GOL304
D	HOH413
D	HOH414
D	HOH428
D	HOH479

site_id	AE2
Number of Residues	12
Details	binding site for residue CYT D 303

Chain	Residue
D	THR93
D	THR94
D	GLY95
D	PHE161
D	GLN165
D	ARG167
D	GLU195
D	MET196
D	ILE220
D	CTN302
D	GOL304
D	HOH488

site_id	AE3
Number of Residues	9
Details	binding site for residue GOL D 304

Chain	Residue
C	HIS7
D	ILE68
D	THR93
D	GLU197
D	CTN302
D	CYT303
D	HOH413
D	HOH414
D	HOH479

site_id	AE4
Number of Residues	4
Details	binding site for residue CL E 301

Chain	Residue
E	ILE220
E	ASN221
E	GLU226
E	HOH515

site_id	AE5
Number of Residues	5
Details	binding site for residue CL E 302

Chain	Residue
E	GLY25
E	ASP26
E	ARG29
E	HOH466
E	HOH599

site_id	AE6
Number of Residues	6
Details	binding site for residue EDO E 303

Chain	Residue
E	ARG178
E	HOH414
E	HOH440
E	HOH451
E	HOH568
F	LEU120

site_id	AE7
Number of Residues	6
Details	binding site for residue K E 304

Chain	Residue
E	GLU48
E	ILE68
E	SER72
F	GLU48
F	ILE68
F	SER72

site_id	AE8
Number of Residues	18
Details	binding site for residue CTN E 305

Chain	Residue
E	THR93
E	THR94
E	GLY95
E	PHE161
E	GLN165
E	ARG167
E	GLU195
E	MET196
E	GLU197
E	ILE220
E	CYT306
E	GOL307
E	HOH405
E	HOH422
E	HOH436
E	HOH480
E	HOH501
F	HIS7

site_id	AE9
Number of Residues	12
Details	binding site for residue CYT E 306

Chain	Residue
E	THR93
E	THR94
E	GLY95
E	PHE161
E	GLN165
E	ARG167
E	GLU195
E	MET196
E	ILE220
E	CTN305
E	GOL307
E	HOH480

site_id	AF1
Number of Residues	9
Details	binding site for residue GOL E 307

Chain	Residue
E	ILE68
E	THR93
E	GLU197
E	CTN305
E	CYT306
E	HOH405
E	HOH422
E	HOH436
F	HIS7

site_id	AF2
Number of Residues	4
Details	binding site for residue CL F 301

Chain	Residue
E	HOH608
F	GLY25
F	ASP26
F	HOH429

site_id	AF3
Number of Residues	17
Details	binding site for residue CTN F 302

Chain	Residue
E	HIS7
F	THR93
F	THR94
F	GLY95
F	PHE161
F	GLN165
F	ARG167
F	GLU195
F	MET196
F	GLU197
F	CYT303
F	GOL304
F	HOH404
F	HOH409
F	HOH416
F	HOH425
F	HOH478

site_id	AF4
Number of Residues	11
Details	binding site for residue CYT F 303

Chain	Residue
F	THR94
F	GLY95
F	PHE161
F	GLN165
F	ARG167
F	GLU195
F	MET196
F	ILE220
F	CTN302
F	GOL304
F	HOH478

site_id	AF5
Number of Residues	9
Details	binding site for residue GOL F 304

Chain	Residue
E	HIS7
F	ILE68
F	THR93
F	GLU197
F	CTN302
F	CYT303
F	HOH409
F	HOH416
F	HOH425

Functional Information from PROSITE/UniProt

site_id	PS01232
Number of Residues	16
Details	PNP_UDP_1 Purine and other phosphorylases family 1 signature. StGIGgPStSIaveEL

Chain	Residue	Details
A	SER65-LEU80

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