Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VR8

Human UDP-Glucose Dehydrogenase with UDP-Xylose Bound to the Co-enzyme Site

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001702	biological_process	gastrulation with mouth forming second
A	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005829	cellular_component	cytosol
A	0006024	biological_process	glycosaminoglycan biosynthetic process
A	0006065	biological_process	UDP-glucuronate biosynthetic process
A	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0030206	biological_process	chondroitin sulfate biosynthetic process
A	0034214	biological_process	protein hexamerization
A	0042802	molecular_function	identical protein binding
A	0048666	biological_process	neuron development
A	0051287	molecular_function	NAD binding
A	0070062	cellular_component	extracellular exosome
B	0001702	biological_process	gastrulation with mouth forming second
B	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005829	cellular_component	cytosol
B	0006024	biological_process	glycosaminoglycan biosynthetic process
B	0006065	biological_process	UDP-glucuronate biosynthetic process
B	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0030206	biological_process	chondroitin sulfate biosynthetic process
B	0034214	biological_process	protein hexamerization
B	0042802	molecular_function	identical protein binding
B	0048666	biological_process	neuron development
B	0051287	molecular_function	NAD binding
B	0070062	cellular_component	extracellular exosome
C	0001702	biological_process	gastrulation with mouth forming second
C	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005829	cellular_component	cytosol
C	0006024	biological_process	glycosaminoglycan biosynthetic process
C	0006065	biological_process	UDP-glucuronate biosynthetic process
C	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0030206	biological_process	chondroitin sulfate biosynthetic process
C	0034214	biological_process	protein hexamerization
C	0042802	molecular_function	identical protein binding
C	0048666	biological_process	neuron development
C	0051287	molecular_function	NAD binding
C	0070062	cellular_component	extracellular exosome
D	0001702	biological_process	gastrulation with mouth forming second
D	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0006024	biological_process	glycosaminoglycan biosynthetic process
D	0006065	biological_process	UDP-glucuronate biosynthetic process
D	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0030206	biological_process	chondroitin sulfate biosynthetic process
D	0034214	biological_process	protein hexamerization
D	0042802	molecular_function	identical protein binding
D	0048666	biological_process	neuron development
D	0051287	molecular_function	NAD binding
D	0070062	cellular_component	extracellular exosome
E	0001702	biological_process	gastrulation with mouth forming second
E	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005829	cellular_component	cytosol
E	0006024	biological_process	glycosaminoglycan biosynthetic process
E	0006065	biological_process	UDP-glucuronate biosynthetic process
E	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
E	0016491	molecular_function	oxidoreductase activity
E	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E	0030206	biological_process	chondroitin sulfate biosynthetic process
E	0034214	biological_process	protein hexamerization
E	0042802	molecular_function	identical protein binding
E	0048666	biological_process	neuron development
E	0051287	molecular_function	NAD binding
E	0070062	cellular_component	extracellular exosome
F	0001702	biological_process	gastrulation with mouth forming second
F	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005829	cellular_component	cytosol
F	0006024	biological_process	glycosaminoglycan biosynthetic process
F	0006065	biological_process	UDP-glucuronate biosynthetic process
F	0015012	biological_process	heparan sulfate proteoglycan biosynthetic process
F	0016491	molecular_function	oxidoreductase activity
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0030206	biological_process	chondroitin sulfate biosynthetic process
F	0034214	biological_process	protein hexamerization
F	0042802	molecular_function	identical protein binding
F	0048666	biological_process	neuron development
F	0051287	molecular_function	NAD binding
F	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	binding site for residue UDX A 501

Chain	Residue
A	GLY11
A	THR91
A	SER130
A	THR131
A	VAL132
A	SER275
A	ARG346
A	HOH601
A	HOH612
A	HOH678
A	HOH705
A	GLY13
A	HOH708
A	HOH747
A	TYR14
A	VAL15
A	ASP36
A	VAL37
A	ARG41
A	VAL89
A	ASN90

site_id	AC2
Number of Residues	26
Details	binding site for residue UDX A 502

Chain	Residue
A	GLU161
A	PHE162
A	LEU163
A	ALA164
A	GLU165
A	LYS220
A	ILE231
A	PHE265
A	LEU266
A	LYS267
A	SER269
A	PHE272
A	GLY273
A	CYS276
A	PHE277
A	PHE338
A	LYS339
A	ARG442
A	HOH636
A	HOH662
A	HOH669
A	HOH679
A	HOH697
A	HOH700
A	HOH766
B	ARG260

site_id	AC3
Number of Residues	23
Details	binding site for residue UDX B 501

Chain	Residue
B	GLY11
B	GLY13
B	TYR14
B	VAL15
B	ASP36
B	VAL37
B	ARG41
B	VAL89
B	ASN90
B	THR91
B	TYR108
B	SER130
B	THR131
B	VAL132
B	SER275
B	LYS279
B	ARG346
B	HOH601
B	HOH615
B	HOH651
B	HOH660
B	HOH676
B	HOH737

site_id	AC4
Number of Residues	27
Details	binding site for residue UDX B 502

Chain	Residue
A	ARG260
B	GLU161
B	PHE162
B	LEU163
B	ALA164
B	GLU165
B	LYS220
B	ILE231
B	PHE265
B	LEU266
B	LYS267
B	SER269
B	PHE272
B	GLY273
B	CYS276
B	PHE277
B	PHE338
B	LYS339
B	ARG442
B	HOH621
B	HOH643
B	HOH655
B	HOH698
B	HOH706
B	HOH738
B	HOH740
B	HOH789

site_id	AC5
Number of Residues	17
Details	binding site for residue ADP C 500

Chain	Residue
C	GLY13
C	TYR14
C	VAL15
C	ASP36
C	VAL37
C	ARG41
C	VAL89
C	ASN90
C	CYS112
C	ARG346
C	HOH658
C	HOH666
C	HOH712
C	HOH735
C	HOH738
C	ILE10
C	GLY11

site_id	AC6
Number of Residues	27
Details	binding site for residue UDX C 501

Chain	Residue
C	GLU161
C	PHE162
C	LEU163
C	ALA164
C	GLU165
C	LYS220
C	ILE231
C	PHE265
C	LEU266
C	LYS267
C	SER269
C	PHE272
C	GLY273
C	CYS276
C	PHE277
C	PHE338
C	LYS339
C	ARG442
C	HOH625
C	HOH639
C	HOH687
C	HOH697
C	HOH706
C	HOH707
C	HOH717
C	HOH731
E	ARG260

site_id	AC7
Number of Residues	21
Details	binding site for residue UDX D 501

Chain	Residue
D	GLY11
D	GLY13
D	TYR14
D	VAL15
D	ASP36
D	VAL37
D	ARG41
D	VAL89
D	ASN90
D	THR91
D	SER130
D	THR131
D	VAL132
D	SER275
D	LYS279
D	ARG346
D	HOH601
D	HOH614
D	HOH659
D	HOH684
D	HOH713

site_id	AC8
Number of Residues	28
Details	binding site for residue UDX D 502

Chain	Residue
D	THR131
D	GLU161
D	PHE162
D	LEU163
D	ALA164
D	GLU165
D	LYS220
D	ILE231
D	PHE265
D	LEU266
D	LYS267
D	SER269
D	PHE272
D	GLY273
D	CYS276
D	PHE277
D	PHE338
D	LYS339
D	ARG442
D	HOH618
D	HOH633
D	HOH655
D	HOH687
D	HOH688
D	HOH717
D	HOH745
D	HOH748
F	ARG260

site_id	AC9
Number of Residues	20
Details	binding site for residue UDX E 501

Chain	Residue
E	GLY11
E	GLY13
E	TYR14
E	VAL15
E	ASP36
E	VAL37
E	ARG41
E	VAL89
E	ASN90
E	THR91
E	SER130
E	THR131
E	VAL132
E	SER275
E	LYS279
E	ARG346
E	HOH601
E	HOH606
E	HOH632
E	HOH635

site_id	AD1
Number of Residues	27
Details	binding site for residue UDX E 502

Chain	Residue
C	ARG260
E	GLU161
E	PHE162
E	LEU163
E	ALA164
E	GLU165
E	LYS220
E	ILE231
E	PHE265
E	LEU266
E	LYS267
E	SER269
E	PHE272
E	GLY273
E	CYS276
E	PHE277
E	PHE338
E	LYS339
E	ARG442
E	HOH617
E	HOH643
E	HOH659
E	HOH660
E	HOH661
E	HOH690
E	HOH712
E	HOH716

site_id	AD2
Number of Residues	17
Details	binding site for residue ADP F 500

Chain	Residue
F	ILE10
F	GLY11
F	GLY13
F	TYR14
F	VAL15
F	ASP36
F	VAL37
F	ARG41
F	VAL89
F	ASN90
F	CYS112
F	ARG346
F	HOH632
F	HOH663
F	HOH664
F	HOH666
F	HOH700

site_id	AD3
Number of Residues	26
Details	binding site for residue UDX F 501

Chain	Residue
D	ARG260
F	GLU161
F	PHE162
F	LEU163
F	ALA164
F	GLU165
F	LYS220
F	ILE231
F	PHE265
F	LEU266
F	LYS267
F	SER269
F	PHE272
F	GLY273
F	CYS276
F	PHE277
F	PHE338
F	LYS339
F	ARG442
F	HOH613
F	HOH645
F	HOH653
F	HOH659
F	HOH685
F	HOH688
F	HOH704

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269\|PubMed:22123821

Chain	Residue	Details
A	GLU161
E	LYS220
F	GLU161
F	LYS220
A	LYS220
B	GLU161
B	LYS220
C	GLU161
C	LYS220
D	GLU161
D	LYS220
E	GLU161

site_id	SWS_FT_FI2
Number of Residues	6
Details	ACT_SITE: Nucleophile => ECO:0000269\|PubMed:21502315, ECO:0000269\|PubMed:21984906, ECO:0000269\|PubMed:22123821

Chain	Residue	Details
A	CYS276
B	CYS276
C	CYS276
D	CYS276
E	CYS276
F	CYS276

site_id	SWS_FT_FI3
Number of Residues	30
Details	BINDING: BINDING => ECO:0000269\|PubMed:21502315, ECO:0000269\|PubMed:21595445, ECO:0000269\|PubMed:21984906, ECO:0007744\|PDB:2Q3E, ECO:0007744\|PDB:2QG4, ECO:0007744\|PDB:3PRJ, ECO:0007744\|PDB:3PTZ, ECO:0007744\|PDB:3TDK

Chain	Residue	Details
A	GLY11
B	CYS276
C	GLY11
C	ASP36
C	ARG41
C	VAL89
C	CYS276
D	GLY11
D	ASP36
D	ARG41
D	VAL89
A	ASP36
D	CYS276
E	GLY11
E	ASP36
E	ARG41
E	VAL89
E	CYS276
F	GLY11
F	ASP36
F	ARG41
F	VAL89
A	ARG41
F	CYS276
A	VAL89
A	CYS276
B	GLY11
B	ASP36
B	ARG41
B	VAL89

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:21502315, ECO:0000269\|PubMed:21595445

Chain	Residue	Details
A	SER130
B	SER130
C	SER130
D	SER130
E	SER130
F	SER130

site_id	SWS_FT_FI5
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:23106432, ECO:0000305\|PubMed:21502315, ECO:0000305\|PubMed:21595445, ECO:0007744\|PDB:2QG4, ECO:0007744\|PDB:3PRJ, ECO:0007744\|PDB:3PTZ, ECO:0007744\|PDB:4EDF

Chain	Residue	Details
A	GLU161
C	LYS220
C	LYS267
C	PHE338
D	GLU161
D	LYS220
D	LYS267
D	PHE338
E	GLU161
E	LYS220
E	LYS267
A	LYS220
E	PHE338
F	GLU161
F	LYS220
F	LYS267
F	PHE338
A	LYS267
A	PHE338
B	GLU161
B	LYS220
B	LYS267
B	PHE338
C	GLU161

site_id	SWS_FT_FI6
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:21502315, ECO:0007744\|PDB:2Q3E, ECO:0007744\|PDB:2QG4

Chain	Residue	Details
A	GLU165
B	GLU165
C	GLU165
D	GLU165
E	GLU165
F	GLU165

site_id	SWS_FT_FI7
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:23106432, ECO:0000269\|PubMed:27966912, ECO:0000305\|PubMed:21502315, ECO:0000305\|PubMed:21595445, ECO:0007744\|PDB:2QG4, ECO:0007744\|PDB:3PRJ, ECO:0007744\|PDB:3PTZ, ECO:0007744\|PDB:4EDF, ECO:0007744\|PDB:5TJH

Chain	Residue	Details
A	ARG260
B	ARG260
C	ARG260
D	ARG260
E	ARG260
F	ARG260

site_id	SWS_FT_FI8
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:21502315, ECO:0000269\|PubMed:21595445, ECO:0000269\|PubMed:21984906, ECO:0000269\|PubMed:22123821, ECO:0007744\|PDB:2Q3E, ECO:0007744\|PDB:2QG4, ECO:0007744\|PDB:3PRJ, ECO:0007744\|PDB:3PTZ, ECO:0007744\|PDB:3TDK

Chain	Residue	Details
A	ARG346
B	ARG346
C	ARG346
D	ARG346
E	ARG346
F	ARG346

site_id	SWS_FT_FI9
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:22123821, ECO:0000269\|PubMed:23106432, ECO:0000305\|PubMed:21502315, ECO:0000305\|PubMed:21595445, ECO:0007744\|PDB:2QG4, ECO:0007744\|PDB:3KHU, ECO:0007744\|PDB:3PRJ, ECO:0007744\|PDB:3PTZ, ECO:0007744\|PDB:4EDF

Chain	Residue	Details
A	ARG442
B	ARG442
C	ARG442
D	ARG442
E	ARG442
F	ARG442

site_id	SWS_FT_FI10
Number of Residues	6
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS107
B	LYS107
C	LYS107
D	LYS107
E	LYS107
F	LYS107

site_id	SWS_FT_FI11
Number of Residues	6
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:24275569

Chain	Residue	Details
A	SER476
B	SER476
C	SER476
D	SER476
E	SER476
F	SER476

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