Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3KHU

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001702	biological_process	gastrulation with mouth forming second
A	0003824	molecular_function	catalytic activity
A	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
A	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
A	0042802	molecular_function	identical protein binding
A	0048666	biological_process	neuron development
A	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
A	0051287	molecular_function	NAD binding
A	0070062	cellular_component	extracellular exosome
B	0001702	biological_process	gastrulation with mouth forming second
B	0003824	molecular_function	catalytic activity
B	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
B	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
B	0042802	molecular_function	identical protein binding
B	0048666	biological_process	neuron development
B	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
B	0051287	molecular_function	NAD binding
B	0070062	cellular_component	extracellular exosome
C	0001702	biological_process	gastrulation with mouth forming second
C	0003824	molecular_function	catalytic activity
C	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
C	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
C	0042802	molecular_function	identical protein binding
C	0048666	biological_process	neuron development
C	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
C	0051287	molecular_function	NAD binding
C	0070062	cellular_component	extracellular exosome
D	0001702	biological_process	gastrulation with mouth forming second
D	0003824	molecular_function	catalytic activity
D	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
D	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
D	0042802	molecular_function	identical protein binding
D	0048666	biological_process	neuron development
D	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
D	0051287	molecular_function	NAD binding
D	0070062	cellular_component	extracellular exosome
E	0001702	biological_process	gastrulation with mouth forming second
E	0003824	molecular_function	catalytic activity
E	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
E	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
E	0042802	molecular_function	identical protein binding
E	0048666	biological_process	neuron development
E	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
E	0051287	molecular_function	NAD binding
E	0070062	cellular_component	extracellular exosome
F	0001702	biological_process	gastrulation with mouth forming second
F	0003824	molecular_function	catalytic activity
F	0003979	molecular_function	UDP-glucose 6-dehydrogenase activity
F	0005634	cellular_component	nucleus
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	0034214	biological_process	protein hexamerization
F	0042802	molecular_function	identical protein binding
F	0048666	biological_process	neuron development
F	0050650	biological_process	chondroitin sulfate proteoglycan biosynthetic process
F	0051287	molecular_function	NAD binding
F	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	30
Details	BINDING SITE FOR RESIDUE UPG A 501

Chain	Residue
A	GLN161
A	LEU266
A	LYS267
A	SER269
A	PHE272
A	GLY273
A	CYS276
A	PHE277
A	PHE338
A	LYS339
A	ARG442
A	PHE162
A	HOH485
A	HOH521
A	HOH530
A	HOH543
A	HOH596
A	EDO615
A	HOH655
A	HOH831
A	HOH951
A	HOH1195
A	LEU163
B	ARG260
A	ALA164
A	GLU165
A	LYS220
A	ASN224
A	ILE231
A	PHE265

site_id	AC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE UPG A 502

Chain	Residue
A	GLY11
A	GLY13
A	TYR14
A	VAL15
A	ASP36
A	VAL37
A	ARG41
A	SER88
A	VAL89
A	ASN90
A	SER130
A	THR131
A	GLN161
A	SER275
A	CYS276
A	ARG346
A	HOH508
A	HOH517
A	HOH565
A	HOH1193

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 611

Chain	Residue
A	PHE2
A	GLU3

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 614

Chain	Residue
A	GLU289
A	ALA297
A	ARG298
A	GLN301
A	HOH886

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 615

Chain	Residue
A	ALA268
A	SER269
A	ARG442
A	UPG501
A	HOH951

site_id	AC6
Number of Residues	27
Details	BINDING SITE FOR RESIDUE UPG B 501

Chain	Residue
A	ARG260
B	GLN161
B	PHE162
B	LEU163
B	ALA164
B	GLU165
B	LYS220
B	ASN224
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	HOH468
B	HOH475
B	HOH504
B	HOH534
B	HOH541
B	EDO608
B	HOH739

site_id	AC7
Number of Residues	19
Details	BINDING SITE FOR RESIDUE UPG B 502

Chain	Residue
B	SER130
B	THR131
B	GLN161
B	SER275
B	CYS276
B	ARG346
B	HOH1027
B	HOH1163
B	HOH1211
B	GLY11
B	GLY13
B	TYR14
B	VAL15
B	ASP36
B	VAL37
B	ASN38
B	ARG41
B	ASN90
B	TYR108

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 601

Chain	Residue
A	GLN229
A	TYR299
A	VAL303
B	GLN229
B	TYR299
B	VAL303

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 602

Chain	Residue
B	THR91
B	ALA104
B	LYS279
B	ASP280

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 607

Chain	Residue
B	GLU249
B	ALA252
B	ASN263
B	HOH546

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 608

Chain	Residue
B	PHE265
B	UPG501
B	HOH541

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 612

Chain	Residue
B	LEU423
B	TYR425
B	GLU451
B	HOH564

site_id	BC4
Number of Residues	28
Details	BINDING SITE FOR RESIDUE UPG C 501

Chain	Residue
C	GLN161
C	PHE162
C	LEU163
C	ALA164
C	GLU165
C	LYS220
C	ASN224
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	HOH504
C	HOH506
C	HOH517
C	HOH625
C	HOH825
C	HOH1000
C	HOH1001
C	HOH1123
D	ARG260

site_id	BC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE UPG C 502

Chain	Residue
C	GLY13
C	TYR14
C	VAL15
C	ASP36
C	VAL37
C	ARG41
C	VAL89
C	ASN90
C	SER130
C	THR131
C	GLN161
C	SER275
C	ARG346
C	HOH484
C	HOH491
C	HOH1008

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 604

Chain	Residue
C	ASP328
C	HIS363
C	HIS365

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 609

Chain	Residue
C	VAL156
C	ASP183
C	THR213

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 616

Chain	Residue
C	GLU289
C	ARG298
C	GLN301
C	HOH902

site_id	BC9
Number of Residues	26
Details	BINDING SITE FOR RESIDUE UPG D 501

Chain	Residue
C	ARG260
C	HOH618
D	PHE162
D	LEU163
D	ALA164
D	GLU165
D	LYS220
D	ASN224
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	HOH521
D	HOH537
D	HOH610
D	HOH991
D	HOH1022
D	HOH1168

site_id	CC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE UPG D 502

Chain	Residue
D	GLY11
D	GLY13
D	TYR14
D	VAL15
D	ASP36
D	VAL37
D	ARG41
D	VAL89
D	ASN90
D	TYR108
D	SER130
D	THR131
D	GLN161
D	SER275
D	ARG346
D	HOH513
D	HOH791
D	HOH953
D	HOH1172
D	HOH1183

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EPE D 618

Chain	Residue
C	GLU184
D	GLY447
D	HIS449
D	ASN450
D	LYS464
D	HOH803

site_id	CC3
Number of Residues	27
Details	BINDING SITE FOR RESIDUE UPG E 501

Chain	Residue
E	PHE162
E	LEU163
E	ALA164
E	GLU165
E	LYS220
E	ASN224
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	HOH473
E	HOH486
E	HOH490
E	UPG502
E	HOH526
E	HOH900
E	HOH1005
E	HOH1182
F	ARG260

site_id	CC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE UPG E 502

Chain	Residue
E	GLY13
E	TYR14
E	VAL15
E	ASP36
E	VAL37
E	ARG41
E	TYR108
E	SER130
E	THR131
E	SER275
E	CYS276
E	ARG346
E	UPG501
E	HOH505
E	HOH518
E	EDO613
E	HOH1176

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO E 603

Chain	Residue
E	ILE52
E	TYR53
E	GLU54
E	GLY56
E	LEU57
E	LYS58
E	GLU59

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO E 605

Chain	Residue
E	HIS363
E	HIS365
E	ARG393
E	LEU394
E	HOH891

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO E 606

Chain	Residue
E	LYS421
E	GLU422
E	LEU423

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO E 610

Chain	Residue
E	ALA268
E	SER269
E	ARG442
E	HOH900

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO E 613

Chain	Residue
E	VAL37
E	ARG115
E	UPG502

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO E 617

Chain	Residue
A	TYR96
E	MET358
E	GLN390
E	ARG393

site_id	DC2
Number of Residues	25
Details	BINDING SITE FOR RESIDUE UPG F 501

Chain	Residue
E	ARG260
F	GLN161
F	PHE162
F	LEU163
F	GLU165
F	LYS220
F	ASN224
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	HOH469
F	HOH480
F	HOH489
F	HOH522
F	HOH760
F	HOH1118

site_id	DC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE UPG F 502

Chain	Residue
F	GLY11
F	GLY13
F	TYR14
F	VAL15
F	ASP36
F	VAL37
F	ARG41
F	VAL89
F	SER130
F	THR131
F	GLN161
F	SER275
F	ARG346
F	HOH490
F	HOH498
F	HOH594

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	132
Details	Region: {"description":"Disordered","evidences":[{"source":"PubMed","id":"23106432","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Region: {"description":"Allosteric switch region","evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21961565","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25478983","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27966912","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30457329","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Region: {"description":"Important for formation of active hexamer structure","evidences":[{"source":"PubMed","id":"25478983","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23106432","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"22123821","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21984906","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22123821","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	84
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21984906","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2Q3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PRJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TDK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	90
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23106432","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PRJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EDF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2Q3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23106432","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27966912","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PRJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EDF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5TJH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21984906","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22123821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2Q3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PRJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TDK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22123821","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23106432","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21502315","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21595445","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2QG4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KHU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PRJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3PTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EDF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	6
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
A	ASP280
A	ASN224
A	THR131
A	CYS276
A	LYS220
A	GLU165

site_id	CSA2
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
B	ASP280
B	ASN224
B	THR131
B	CYS276
B	LYS220
B	GLU165

site_id	CSA3
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
C	ASP280
C	ASN224
C	THR131
C	CYS276
C	LYS220
C	GLU165

site_id	CSA4
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
D	ASP280
D	ASN224
D	THR131
D	CYS276
D	LYS220
D	GLU165

site_id	CSA5
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
E	ASP280
E	ASN224
E	THR131
E	CYS276
E	LYS220
E	GLU165

site_id	CSA6
Number of Residues	6
Details	Annotated By Reference To The Literature 1dli

Chain	Residue	Details
F	ASP280
F	ASN224
F	THR131
F	CYS276
F	LYS220
F	GLU165

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