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3KHU

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0001702biological_processgastrulation with mouth forming second
A0003979molecular_functionUDP-glucose 6-dehydrogenase activity
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005829cellular_componentcytosol
A0006024biological_processglycosaminoglycan biosynthetic process
A0006065biological_processUDP-glucuronate biosynthetic process
A0015012biological_processheparan sulfate proteoglycan biosynthetic process
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0030206biological_processchondroitin sulfate biosynthetic process
A0034214biological_processprotein hexamerization
A0042802molecular_functionidentical protein binding
A0048666biological_processneuron development
A0051287molecular_functionNAD binding
A0070062cellular_componentextracellular exosome
B0001702biological_processgastrulation with mouth forming second
B0003979molecular_functionUDP-glucose 6-dehydrogenase activity
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005829cellular_componentcytosol
B0006024biological_processglycosaminoglycan biosynthetic process
B0006065biological_processUDP-glucuronate biosynthetic process
B0015012biological_processheparan sulfate proteoglycan biosynthetic process
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0030206biological_processchondroitin sulfate biosynthetic process
B0034214biological_processprotein hexamerization
B0042802molecular_functionidentical protein binding
B0048666biological_processneuron development
B0051287molecular_functionNAD binding
B0070062cellular_componentextracellular exosome
C0001702biological_processgastrulation with mouth forming second
C0003979molecular_functionUDP-glucose 6-dehydrogenase activity
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005829cellular_componentcytosol
C0006024biological_processglycosaminoglycan biosynthetic process
C0006065biological_processUDP-glucuronate biosynthetic process
C0015012biological_processheparan sulfate proteoglycan biosynthetic process
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0030206biological_processchondroitin sulfate biosynthetic process
C0034214biological_processprotein hexamerization
C0042802molecular_functionidentical protein binding
C0048666biological_processneuron development
C0051287molecular_functionNAD binding
C0070062cellular_componentextracellular exosome
D0001702biological_processgastrulation with mouth forming second
D0003979molecular_functionUDP-glucose 6-dehydrogenase activity
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005829cellular_componentcytosol
D0006024biological_processglycosaminoglycan biosynthetic process
D0006065biological_processUDP-glucuronate biosynthetic process
D0015012biological_processheparan sulfate proteoglycan biosynthetic process
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0030206biological_processchondroitin sulfate biosynthetic process
D0034214biological_processprotein hexamerization
D0042802molecular_functionidentical protein binding
D0048666biological_processneuron development
D0051287molecular_functionNAD binding
D0070062cellular_componentextracellular exosome
E0001702biological_processgastrulation with mouth forming second
E0003979molecular_functionUDP-glucose 6-dehydrogenase activity
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005829cellular_componentcytosol
E0006024biological_processglycosaminoglycan biosynthetic process
E0006065biological_processUDP-glucuronate biosynthetic process
E0015012biological_processheparan sulfate proteoglycan biosynthetic process
E0016491molecular_functionoxidoreductase activity
E0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E0030206biological_processchondroitin sulfate biosynthetic process
E0034214biological_processprotein hexamerization
E0042802molecular_functionidentical protein binding
E0048666biological_processneuron development
E0051287molecular_functionNAD binding
E0070062cellular_componentextracellular exosome
F0001702biological_processgastrulation with mouth forming second
F0003979molecular_functionUDP-glucose 6-dehydrogenase activity
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005829cellular_componentcytosol
F0006024biological_processglycosaminoglycan biosynthetic process
F0006065biological_processUDP-glucuronate biosynthetic process
F0015012biological_processheparan sulfate proteoglycan biosynthetic process
F0016491molecular_functionoxidoreductase activity
F0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F0030206biological_processchondroitin sulfate biosynthetic process
F0034214biological_processprotein hexamerization
F0042802molecular_functionidentical protein binding
F0048666biological_processneuron development
F0051287molecular_functionNAD binding
F0070062cellular_componentextracellular exosome
Functional Information from PDB Data
site_idAC1
Number of Residues30
DetailsBINDING SITE FOR RESIDUE UPG A 501
ChainResidue
AGLN161
ALEU266
ALYS267
ASER269
APHE272
AGLY273
ACYS276
APHE277
APHE338
ALYS339
AARG442
APHE162
AHOH485
AHOH521
AHOH530
AHOH543
AHOH596
AEDO615
AHOH655
AHOH831
AHOH951
AHOH1195
ALEU163
BARG260
AALA164
AGLU165
ALYS220
AASN224
AILE231
APHE265

site_idAC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE UPG A 502
ChainResidue
AGLY11
AGLY13
ATYR14
AVAL15
AASP36
AVAL37
AARG41
ASER88
AVAL89
AASN90
ASER130
ATHR131
AGLN161
ASER275
ACYS276
AARG346
AHOH508
AHOH517
AHOH565
AHOH1193

site_idAC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 611
ChainResidue
APHE2
AGLU3

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 614
ChainResidue
AGLU289
AALA297
AARG298
AGLN301
AHOH886

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 615
ChainResidue
AALA268
ASER269
AARG442
AUPG501
AHOH951

site_idAC6
Number of Residues27
DetailsBINDING SITE FOR RESIDUE UPG B 501
ChainResidue
AARG260
BGLN161
BPHE162
BLEU163
BALA164
BGLU165
BLYS220
BASN224
BILE231
BPHE265
BLEU266
BLYS267
BSER269
BPHE272
BGLY273
BCYS276
BPHE277
BPHE338
BLYS339
BARG442
BHOH468
BHOH475
BHOH504
BHOH534
BHOH541
BEDO608
BHOH739

site_idAC7
Number of Residues19
DetailsBINDING SITE FOR RESIDUE UPG B 502
ChainResidue
BSER130
BTHR131
BGLN161
BSER275
BCYS276
BARG346
BHOH1027
BHOH1163
BHOH1211
BGLY11
BGLY13
BTYR14
BVAL15
BASP36
BVAL37
BASN38
BARG41
BASN90
BTYR108

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 601
ChainResidue
AGLN229
ATYR299
AVAL303
BGLN229
BTYR299
BVAL303

site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 602
ChainResidue
BTHR91
BALA104
BLYS279
BASP280

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 607
ChainResidue
BGLU249
BALA252
BASN263
BHOH546

site_idBC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 608
ChainResidue
BPHE265
BUPG501
BHOH541

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 612
ChainResidue
BLEU423
BTYR425
BGLU451
BHOH564

site_idBC4
Number of Residues28
DetailsBINDING SITE FOR RESIDUE UPG C 501
ChainResidue
CGLN161
CPHE162
CLEU163
CALA164
CGLU165
CLYS220
CASN224
CILE231
CPHE265
CLEU266
CLYS267
CSER269
CPHE272
CGLY273
CCYS276
CPHE277
CPHE338
CLYS339
CARG442
CHOH504
CHOH506
CHOH517
CHOH625
CHOH825
CHOH1000
CHOH1001
CHOH1123
DARG260

site_idBC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE UPG C 502
ChainResidue
CGLY13
CTYR14
CVAL15
CASP36
CVAL37
CARG41
CVAL89
CASN90
CSER130
CTHR131
CGLN161
CSER275
CARG346
CHOH484
CHOH491
CHOH1008

site_idBC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO C 604
ChainResidue
CASP328
CHIS363
CHIS365

site_idBC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO C 609
ChainResidue
CVAL156
CASP183
CTHR213

site_idBC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 616
ChainResidue
CGLU289
CARG298
CGLN301
CHOH902

site_idBC9
Number of Residues26
DetailsBINDING SITE FOR RESIDUE UPG D 501
ChainResidue
CARG260
CHOH618
DPHE162
DLEU163
DALA164
DGLU165
DLYS220
DASN224
DILE231
DPHE265
DLEU266
DLYS267
DSER269
DPHE272
DGLY273
DCYS276
DPHE277
DPHE338
DLYS339
DARG442
DHOH521
DHOH537
DHOH610
DHOH991
DHOH1022
DHOH1168

site_idCC1
Number of Residues20
DetailsBINDING SITE FOR RESIDUE UPG D 502
ChainResidue
DGLY11
DGLY13
DTYR14
DVAL15
DASP36
DVAL37
DARG41
DVAL89
DASN90
DTYR108
DSER130
DTHR131
DGLN161
DSER275
DARG346
DHOH513
DHOH791
DHOH953
DHOH1172
DHOH1183

site_idCC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EPE D 618
ChainResidue
CGLU184
DGLY447
DHIS449
DASN450
DLYS464
DHOH803

site_idCC3
Number of Residues27
DetailsBINDING SITE FOR RESIDUE UPG E 501
ChainResidue
EPHE162
ELEU163
EALA164
EGLU165
ELYS220
EASN224
EILE231
EPHE265
ELEU266
ELYS267
ESER269
EPHE272
EGLY273
ECYS276
EPHE277
EPHE338
ELYS339
EARG442
EHOH473
EHOH486
EHOH490
EUPG502
EHOH526
EHOH900
EHOH1005
EHOH1182
FARG260

site_idCC4
Number of Residues17
DetailsBINDING SITE FOR RESIDUE UPG E 502
ChainResidue
EGLY13
ETYR14
EVAL15
EASP36
EVAL37
EARG41
ETYR108
ESER130
ETHR131
ESER275
ECYS276
EARG346
EUPG501
EHOH505
EHOH518
EEDO613
EHOH1176

site_idCC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO E 603
ChainResidue
EILE52
ETYR53
EGLU54
EGLY56
ELEU57
ELYS58
EGLU59

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO E 605
ChainResidue
EHIS363
EHIS365
EARG393
ELEU394
EHOH891

site_idCC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO E 606
ChainResidue
ELYS421
EGLU422
ELEU423

site_idCC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO E 610
ChainResidue
EALA268
ESER269
EARG442
EHOH900

site_idCC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO E 613
ChainResidue
EVAL37
EARG115
EUPG502

site_idDC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO E 617
ChainResidue
ATYR96
EMET358
EGLN390
EARG393

site_idDC2
Number of Residues25
DetailsBINDING SITE FOR RESIDUE UPG F 501
ChainResidue
EARG260
FGLN161
FPHE162
FLEU163
FGLU165
FLYS220
FASN224
FILE231
FPHE265
FLEU266
FLYS267
FSER269
FPHE272
FGLY273
FCYS276
FPHE277
FPHE338
FLYS339
FARG442
FHOH469
FHOH480
FHOH489
FHOH522
FHOH760
FHOH1118

site_idDC3
Number of Residues16
DetailsBINDING SITE FOR RESIDUE UPG F 502
ChainResidue
FGLY11
FGLY13
FTYR14
FVAL15
FASP36
FVAL37
FARG41
FVAL89
FSER130
FTHR131
FGLN161
FSER275
FARG346
FHOH490
FHOH498
FHOH594

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:22123821
ChainResidueDetails
AGLN161
ELYS220
FGLN161
FLYS220
ALYS220
BGLN161
BLYS220
CGLN161
CLYS220
DGLN161
DLYS220
EGLN161

site_idSWS_FT_FI2
Number of Residues6
DetailsACT_SITE: Nucleophile => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21984906, ECO:0000269|PubMed:22123821
ChainResidueDetails
ACYS276
BCYS276
CCYS276
DCYS276
ECYS276
FCYS276

site_idSWS_FT_FI3
Number of Residues30
DetailsBINDING: 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
ChainResidueDetails
AGLY11
BCYS276
CGLY11
CASP36
CARG41
CVAL89
CCYS276
DGLY11
DASP36
DARG41
DVAL89
AASP36
DCYS276
EGLY11
EASP36
EARG41
EVAL89
ECYS276
FGLY11
FASP36
FARG41
FVAL89
AARG41
FCYS276
AVAL89
ACYS276
BGLY11
BASP36
BARG41
BVAL89

site_idSWS_FT_FI4
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21595445
ChainResidueDetails
ASER130
BSER130
CSER130
DSER130
ESER130
FSER130

site_idSWS_FT_FI5
Number of Residues24
DetailsBINDING: 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
ChainResidueDetails
AGLN161
CLYS220
CLYS267
CPHE338
DGLN161
DLYS220
DLYS267
DPHE338
EGLN161
ELYS220
ELYS267
ALYS220
EPHE338
FGLN161
FLYS220
FLYS267
FPHE338
ALYS267
APHE338
BGLN161
BLYS220
BLYS267
BPHE338
CGLN161

site_idSWS_FT_FI6
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0007744|PDB:2Q3E, ECO:0007744|PDB:2QG4
ChainResidueDetails
AGLU165
BGLU165
CGLU165
DGLU165
EGLU165
FGLU165

site_idSWS_FT_FI7
Number of Residues6
DetailsBINDING: 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
ChainResidueDetails
AARG260
BARG260
CARG260
DARG260
EARG260
FARG260

site_idSWS_FT_FI8
Number of Residues6
DetailsBINDING: 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
ChainResidueDetails
AARG346
BARG346
CARG346
DARG346
EARG346
FARG346

site_idSWS_FT_FI9
Number of Residues6
DetailsBINDING: 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
ChainResidueDetails
AARG442
BARG442
CARG442
DARG442
EARG442
FARG442

site_idSWS_FT_FI10
Number of Residues6
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS107
BLYS107
CLYS107
DLYS107
ELYS107
FLYS107

Catalytic Information from CSA
site_idCSA1
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
AASP280
AASN224
ATHR131
ACYS276
ALYS220
AGLU165

site_idCSA2
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
BASP280
BASN224
BTHR131
BCYS276
BLYS220
BGLU165

site_idCSA3
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
CASP280
CASN224
CTHR131
CCYS276
CLYS220
CGLU165

site_idCSA4
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
DASP280
DASN224
DTHR131
DCYS276
DLYS220
DGLU165

site_idCSA5
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
EASP280
EASN224
ETHR131
ECYS276
ELYS220
EGLU165

site_idCSA6
Number of Residues6
DetailsAnnotated By Reference To The Literature 1dli
ChainResidueDetails
FASP280
FASN224
FTHR131
FCYS276
FLYS220
FGLU165

227344

PDB entries from 2024-11-13

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