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1GT8

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0002058molecular_functionuracil binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006210biological_processthymine catabolic process
A0006212biological_processuracil catabolic process
A0006214biological_processthymidine catabolic process
A0010181molecular_functionFMN binding
A0016491molecular_functionoxidoreductase activity
A0016627molecular_functionoxidoreductase activity, acting on the CH-CH group of donors
A0017113molecular_functiondihydropyrimidine dehydrogenase (NADP+) activity
A0019483biological_processbeta-alanine biosynthetic process
A0042803molecular_functionprotein homodimerization activity
A0046872molecular_functionmetal ion binding
A0050660molecular_functionflavin adenine dinucleotide binding
A0050661molecular_functionNADP binding
A0051536molecular_functioniron-sulfur cluster binding
A0051539molecular_function4 iron, 4 sulfur cluster binding
B0000166molecular_functionnucleotide binding
B0002058molecular_functionuracil binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006210biological_processthymine catabolic process
B0006212biological_processuracil catabolic process
B0006214biological_processthymidine catabolic process
B0010181molecular_functionFMN binding
B0016491molecular_functionoxidoreductase activity
B0016627molecular_functionoxidoreductase activity, acting on the CH-CH group of donors
B0017113molecular_functiondihydropyrimidine dehydrogenase (NADP+) activity
B0019483biological_processbeta-alanine biosynthetic process
B0042803molecular_functionprotein homodimerization activity
B0046872molecular_functionmetal ion binding
B0050660molecular_functionflavin adenine dinucleotide binding
B0050661molecular_functionNADP binding
B0051536molecular_functioniron-sulfur cluster binding
B0051539molecular_function4 iron, 4 sulfur cluster binding
C0000166molecular_functionnucleotide binding
C0002058molecular_functionuracil binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006210biological_processthymine catabolic process
C0006212biological_processuracil catabolic process
C0006214biological_processthymidine catabolic process
C0010181molecular_functionFMN binding
C0016491molecular_functionoxidoreductase activity
C0016627molecular_functionoxidoreductase activity, acting on the CH-CH group of donors
C0017113molecular_functiondihydropyrimidine dehydrogenase (NADP+) activity
C0019483biological_processbeta-alanine biosynthetic process
C0042803molecular_functionprotein homodimerization activity
C0046872molecular_functionmetal ion binding
C0050660molecular_functionflavin adenine dinucleotide binding
C0050661molecular_functionNADP binding
C0051536molecular_functioniron-sulfur cluster binding
C0051539molecular_function4 iron, 4 sulfur cluster binding
D0000166molecular_functionnucleotide binding
D0002058molecular_functionuracil binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006210biological_processthymine catabolic process
D0006212biological_processuracil catabolic process
D0006214biological_processthymidine catabolic process
D0010181molecular_functionFMN binding
D0016491molecular_functionoxidoreductase activity
D0016627molecular_functionoxidoreductase activity, acting on the CH-CH group of donors
D0017113molecular_functiondihydropyrimidine dehydrogenase (NADP+) activity
D0019483biological_processbeta-alanine biosynthetic process
D0042803molecular_functionprotein homodimerization activity
D0046872molecular_functionmetal ion binding
D0050660molecular_functionflavin adenine dinucleotide binding
D0050661molecular_functionNADP binding
D0051536molecular_functioniron-sulfur cluster binding
D0051539molecular_function4 iron, 4 sulfur cluster binding
Functional Information from PDB Data
site_idAC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 A1026
ChainResidue
ACYS91
AGLN156
APRO92
ALEU95
AILE97
AASN120
ACYS130
ATHR132
ALEU135
ACYS136

site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 A1027
ChainResidue
ACYS79
ALEU80
ALYS81
ACYS82
APRO86
ACYS87
ACYS140
AASN141
AILE150
AILE152

site_idAC3
Number of Residues12
DetailsBINDING SITE FOR RESIDUE SF4 A1028
ChainResidue
AILE948
ACYS953
AILE954
AASN955
ACYS956
AGLY957
ALYS958
ACYS959
ACYS996
APRO997
ACYS1001
AILE1002

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 A1029
ChainResidue
ACYS963
ATYR968
AILE971
AVAL982
ACYS986
ATHR987
AGLY988
ACYS989
ATHR990
ACYS992

site_idAC5
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FMN A1030
ChainResidue
AALA549
ASER550
AALA551
ALYS574
ATHR575
AILE590
AASN609
AGLU611
AASN668
ALYS709
ATHR737
ASER766
AGLY767
ATHR793
AGLY794
AGLY795
ACYS816
ASER817
AGLN820
AUAA1035

site_idAC6
Number of Residues26
DetailsBINDING SITE FOR RESIDUE FAD A1031
ChainResidue
AVAL129
AGLY194
AGLY196
APRO197
AALA198
APHE217
AGLU218
ALYS219
AGLN220
AGLY225
ALEU226
AGLU230
AILE231
AARG235
ASER260
ALEU261
AILE283
ALEU310
ATHR343
AASP346
AGLY480
AASP481
ATHR488
ATHR489
ASER492
ANDP1032

site_idAC7
Number of Residues13
DetailsBINDING SITE FOR RESIDUE NDP A1032
ChainResidue
AASN487
AFAD1031
APRO131
AALA340
AGLY341
AASP342
ATHR343
AARG364
ALYS365
AARG371
AALA437
APHE438
AGLY439

site_idAC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE UAA A1035
ChainResidue
AASN609
AGLU611
ALEU612
AILE613
AASN668
ASER670
AASN736
AGLY764
AFMN1030

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 B1026
ChainResidue
BCYS91
BPRO92
BLEU95
BILE97
BASN120
BCYS130
BTHR132
BCYS136
BGLN156

site_idBC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 B1027
ChainResidue
BCYS79
BLEU80
BLYS81
BCYS82
BPRO86
BCYS87
BCYS140
BASN141
BLEU142
BILE150
BILE152

site_idBC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 B1028
ChainResidue
BILE948
BCYS953
BILE954
BCYS956
BGLY957
BLYS958
BCYS959
BCYS996
BPRO997
BCYS1001
BILE1002

site_idBC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 B1029
ChainResidue
BCYS963
BTYR968
BILE971
BVAL982
BCYS986
BTHR987
BGLY988
BCYS989
BTHR990
BCYS992

site_idBC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE FMN B1030
ChainResidue
BALA549
BSER550
BALA551
BLYS574
BTHR575
BILE590
BASN609
BASN668
BLYS709
BTHR735
BASN736
BTHR737
BSER766
BGLY767
BTHR793
BGLY794
BGLY795
BCYS816
BSER817
BGLN820
BUAA1035

site_idBC5
Number of Residues27
DetailsBINDING SITE FOR RESIDUE FAD B1031
ChainResidue
BVAL129
BGLY194
BGLY196
BPRO197
BALA198
BPHE217
BGLU218
BLYS219
BGLN220
BGLY225
BLEU226
BGLU230
BILE231
BARG235
BLYS259
BSER260
BLEU261
BILE283
BLEU310
BTHR343
BASP346
BGLY480
BASP481
BTHR488
BTHR489
BSER492
BNDP1032

site_idBC6
Number of Residues14
DetailsBINDING SITE FOR RESIDUE NDP B1032
ChainResidue
BPRO131
BALA340
BGLY341
BASP342
BTHR343
BARG364
BLYS365
BARG371
BPRO393
BALA437
BPHE438
BGLY439
BASN487
BFAD1031

site_idBC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE UAA B1035
ChainResidue
BASN609
BGLU611
BILE613
BASN668
BSER670
BASN736
BTHR737
BGLY764
BFMN1030

site_idBC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 C1026
ChainResidue
CCYS91
CPRO92
CLEU95
CILE97
CCYS130
CTHR132
CLEU135
CCYS136
CGLN156

site_idBC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 C1027
ChainResidue
CCYS79
CLEU80
CLYS81
CCYS82
CCYS87
CCYS140
CASN141
CILE150
CILE152

site_idCC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 C1028
ChainResidue
CILE948
CCYS953
CILE954
CCYS956
CGLY957
CLYS958
CCYS959
CCYS996
CPRO997
CCYS1001
CILE1002

site_idCC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 C1029
ChainResidue
CCYS963
CTYR968
CILE971
CVAL982
CCYS986
CTHR987
CGLY988
CCYS989
CTHR990
CCYS992

site_idCC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FMN C1030
ChainResidue
CALA549
CSER550
CALA551
CLYS574
CTHR575
CILE590
CASN609
CASN668
CLYS709
CASN736
CSER766
CGLY767
CTHR793
CGLY794
CGLY795
CCYS816
CSER817
CGLN820
CUAA1035

site_idCC4
Number of Residues27
DetailsBINDING SITE FOR RESIDUE FAD C1031
ChainResidue
CVAL129
CGLY194
CGLY196
CPRO197
CALA198
CPHE217
CGLU218
CLYS219
CGLN220
CGLY225
CLEU226
CGLU230
CILE231
CARG235
CSER260
CLEU261
CGLY282
CILE283
CLEU310
CTHR343
CASP346
CGLY480
CASP481
CTHR488
CTHR489
CSER492
CNDP1032

site_idCC5
Number of Residues14
DetailsBINDING SITE FOR RESIDUE NDP C1032
ChainResidue
CPRO131
CALA340
CGLY341
CASP342
CTHR343
CARG364
CLYS365
CARG371
CALA437
CPHE438
CGLY439
CASN487
CTHR488
CFAD1031

site_idCC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE UAA C1035
ChainResidue
CASN609
CGLU611
CLEU612
CILE613
CASN668
CSER670
CASN736
CTHR737
CGLY764
CFMN1030

site_idCC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 D1026
ChainResidue
DCYS91
DPRO92
DLEU95
DILE97
DASN120
DCYS130
DTHR132
DCYS136
DGLN156

site_idCC8
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 D1027
ChainResidue
DCYS79
DLEU80
DLYS81
DCYS82
DPRO86
DCYS87
DCYS140
DASN141
DLEU142
DILE150
DILE152

site_idCC9
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 D1028
ChainResidue
DILE948
DCYS953
DILE954
DCYS956
DGLY957
DLYS958
DCYS959
DCYS996
DPRO997
DCYS1001
DILE1002

site_idDC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 D1029
ChainResidue
DCYS963
DTYR968
DILE971
DVAL982
DCYS986
DTHR987
DGLY988
DCYS989
DTHR990
DCYS992

site_idDC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FMN D1030
ChainResidue
DALA549
DSER550
DALA551
DLYS574
DTHR575
DILE590
DASN609
DASN668
DLYS709
DTHR735
DTHR737
DSER766
DGLY767
DTHR793
DGLY794
DGLY795
DCYS816
DSER817
DGLN820
DUAA1035

site_idDC3
Number of Residues27
DetailsBINDING SITE FOR RESIDUE FAD D1031
ChainResidue
DVAL129
DGLY194
DGLY196
DPRO197
DALA198
DPHE217
DGLU218
DLYS219
DGLN220
DGLY225
DLEU226
DGLU230
DILE231
DARG235
DLYS259
DSER260
DLEU261
DILE283
DLEU310
DTHR343
DASP346
DGLY480
DASP481
DTHR488
DTHR489
DSER492
DNDP1032

site_idDC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE NDP D1032
ChainResidue
DPRO131
DALA340
DGLY341
DASP342
DTHR343
DARG364
DLYS365
DARG371
DPRO393
DALA437
DPHE438
DGLY439
DASN487
DTHR488
DFAD1031

site_idDC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE UAA D1035
ChainResidue
DASN609
DGLU611
DILE613
DASN668
DASN736
DTHR737
DFMN1030

Functional Information from PROSITE/UniProt
site_idPS00198
Number of Residues12
Details4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CtGCTlCLsVCP
ChainResidueDetails
ACYS986-PRO997

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Proton acceptor => ECO:0000269|PubMed:11796730
ChainResidueDetails
ACYS671
BCYS671
CCYS671
DCYS671

site_idSWS_FT_FI2
Number of Residues76
DetailsBINDING:
ChainResidueDetails
ACYS79
AASN668
AASN736
ACYS953
ACYS956
ACYS959
ACYS963
ACYS986
ACYS989
ACYS992
ACYS996
ACYS82
BCYS79
BCYS82
BCYS87
BCYS91
BCYS130
BCYS136
BCYS140
BGLN156
BASN609
BASN668
ACYS87
BASN736
BCYS953
BCYS956
BCYS959
BCYS963
BCYS986
BCYS989
BCYS992
BCYS996
CCYS79
ACYS91
CCYS82
CCYS87
CCYS91
CCYS130
CCYS136
CCYS140
CGLN156
CASN609
CASN668
CASN736
ACYS130
CCYS953
CCYS956
CCYS959
CCYS963
CCYS986
CCYS989
CCYS992
CCYS996
DCYS79
DCYS82
ACYS136
DCYS87
DCYS91
DCYS130
DCYS136
DCYS140
DGLN156
DASN609
DASN668
DASN736
DCYS953
ACYS140
DCYS956
DCYS959
DCYS963
DCYS986
DCYS989
DCYS992
DCYS996
AGLN156
AASN609

site_idSWS_FT_FI3
Number of Residues68
DetailsBINDING: BINDING => ECO:0000269|PubMed:11796730
ChainResidueDetails
AVAL129
AGLY480
AASP481
ASER550
ALYS574
ALYS709
AGLY767
ATHR793
ACYS816
BVAL129
BGLY194
AGLY194
BGLU218
BARG235
BLEU261
BALA340
BARG364
BARG371
BALA437
BGLY480
BASP481
BSER550
AGLU218
BLYS574
BLYS709
BGLY767
BTHR793
BCYS816
CVAL129
CGLY194
CGLU218
CARG235
CLEU261
AARG235
CALA340
CARG364
CARG371
CALA437
CGLY480
CASP481
CSER550
CLYS574
CLYS709
CGLY767
ALEU261
CTHR793
CCYS816
DVAL129
DGLY194
DGLU218
DARG235
DLEU261
DALA340
DARG364
DARG371
AALA340
DALA437
DGLY480
DASP481
DSER550
DLYS574
DLYS709
DGLY767
DTHR793
DCYS816
AARG364
AARG371
AALA437

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q12882
ChainResidueDetails
ALYS384
BLYS384
CLYS384
DLYS384

Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 800
ChainResidueDetails
ALYS574electrostatic stabiliser
ACYS671proton acceptor, proton donor
ALYS709electrostatic stabiliser

site_idMCSA2
Number of Residues3
DetailsM-CSA 800
ChainResidueDetails
BLYS574electrostatic stabiliser
BCYS671proton acceptor, proton donor
BLYS709electrostatic stabiliser

site_idMCSA3
Number of Residues3
DetailsM-CSA 800
ChainResidueDetails
CLYS574electrostatic stabiliser
CCYS671proton acceptor, proton donor
CLYS709electrostatic stabiliser

site_idMCSA4
Number of Residues3
DetailsM-CSA 800
ChainResidueDetails
DLYS574electrostatic stabiliser
DCYS671proton acceptor, proton donor
DLYS709electrostatic stabiliser

218853

PDB entries from 2024-04-24

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