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1YRQ

Structure of the ready oxidized form of [NiFe]-hydrogenase

Functional Information from GO Data
ChainGOidnamespacecontents
A0008901molecular_functionferredoxin hydrogenase activity
A0009055molecular_functionelectron transfer activity
A0009061biological_processanaerobic respiration
A0009375cellular_componentferredoxin hydrogenase complex
A0016020cellular_componentmembrane
A0016491molecular_functionoxidoreductase activity
A0042597cellular_componentperiplasmic space
A0044569cellular_component[Ni-Fe] hydrogenase complex
A0046872molecular_functionmetal ion binding
A0047806molecular_functioncytochrome-c3 hydrogenase activity
A0051536molecular_functioniron-sulfur cluster binding
A0051538molecular_function3 iron, 4 sulfur cluster binding
A0051539molecular_function4 iron, 4 sulfur cluster binding
B0008901molecular_functionferredoxin hydrogenase activity
B0009055molecular_functionelectron transfer activity
B0009061biological_processanaerobic respiration
B0009375cellular_componentferredoxin hydrogenase complex
B0016020cellular_componentmembrane
B0016491molecular_functionoxidoreductase activity
B0042597cellular_componentperiplasmic space
B0044569cellular_component[Ni-Fe] hydrogenase complex
B0046872molecular_functionmetal ion binding
B0047806molecular_functioncytochrome-c3 hydrogenase activity
B0051536molecular_functioniron-sulfur cluster binding
B0051538molecular_function3 iron, 4 sulfur cluster binding
B0051539molecular_function4 iron, 4 sulfur cluster binding
C0008901molecular_functionferredoxin hydrogenase activity
C0009055molecular_functionelectron transfer activity
C0009061biological_processanaerobic respiration
C0009375cellular_componentferredoxin hydrogenase complex
C0016020cellular_componentmembrane
C0016491molecular_functionoxidoreductase activity
C0042597cellular_componentperiplasmic space
C0044569cellular_component[Ni-Fe] hydrogenase complex
C0046872molecular_functionmetal ion binding
C0047806molecular_functioncytochrome-c3 hydrogenase activity
C0051536molecular_functioniron-sulfur cluster binding
C0051538molecular_function3 iron, 4 sulfur cluster binding
C0051539molecular_function4 iron, 4 sulfur cluster binding
D0008901molecular_functionferredoxin hydrogenase activity
D0009055molecular_functionelectron transfer activity
D0009061biological_processanaerobic respiration
D0009375cellular_componentferredoxin hydrogenase complex
D0016020cellular_componentmembrane
D0016491molecular_functionoxidoreductase activity
D0042597cellular_componentperiplasmic space
D0044569cellular_component[Ni-Fe] hydrogenase complex
D0046872molecular_functionmetal ion binding
D0047806molecular_functioncytochrome-c3 hydrogenase activity
D0051536molecular_functioniron-sulfur cluster binding
D0051538molecular_function3 iron, 4 sulfur cluster binding
D0051539molecular_function4 iron, 4 sulfur cluster binding
F0008901molecular_functionferredoxin hydrogenase activity
F0009055molecular_functionelectron transfer activity
F0009061biological_processanaerobic respiration
F0009375cellular_componentferredoxin hydrogenase complex
F0016020cellular_componentmembrane
F0016491molecular_functionoxidoreductase activity
F0042597cellular_componentperiplasmic space
F0044569cellular_component[Ni-Fe] hydrogenase complex
F0046872molecular_functionmetal ion binding
F0047806molecular_functioncytochrome-c3 hydrogenase activity
F0051536molecular_functioniron-sulfur cluster binding
F0051538molecular_function3 iron, 4 sulfur cluster binding
F0051539molecular_function4 iron, 4 sulfur cluster binding
G0008901molecular_functionferredoxin hydrogenase activity
G0009055molecular_functionelectron transfer activity
G0009061biological_processanaerobic respiration
G0009375cellular_componentferredoxin hydrogenase complex
G0016020cellular_componentmembrane
G0016491molecular_functionoxidoreductase activity
G0042597cellular_componentperiplasmic space
G0044569cellular_component[Ni-Fe] hydrogenase complex
G0046872molecular_functionmetal ion binding
G0047806molecular_functioncytochrome-c3 hydrogenase activity
G0051536molecular_functioniron-sulfur cluster binding
G0051538molecular_function3 iron, 4 sulfur cluster binding
G0051539molecular_function4 iron, 4 sulfur cluster binding
H0008901molecular_functionferredoxin hydrogenase activity
H0016151molecular_functionnickel cation binding
H0016491molecular_functionoxidoreductase activity
H0042597cellular_componentperiplasmic space
H0046872molecular_functionmetal ion binding
H0047806molecular_functioncytochrome-c3 hydrogenase activity
I0008901molecular_functionferredoxin hydrogenase activity
I0016151molecular_functionnickel cation binding
I0016491molecular_functionoxidoreductase activity
I0042597cellular_componentperiplasmic space
I0046872molecular_functionmetal ion binding
I0047806molecular_functioncytochrome-c3 hydrogenase activity
J0008901molecular_functionferredoxin hydrogenase activity
J0016151molecular_functionnickel cation binding
J0016491molecular_functionoxidoreductase activity
J0042597cellular_componentperiplasmic space
J0046872molecular_functionmetal ion binding
J0047806molecular_functioncytochrome-c3 hydrogenase activity
K0008901molecular_functionferredoxin hydrogenase activity
K0016151molecular_functionnickel cation binding
K0016491molecular_functionoxidoreductase activity
K0042597cellular_componentperiplasmic space
K0046872molecular_functionmetal ion binding
K0047806molecular_functioncytochrome-c3 hydrogenase activity
M0008901molecular_functionferredoxin hydrogenase activity
M0016151molecular_functionnickel cation binding
M0016491molecular_functionoxidoreductase activity
M0042597cellular_componentperiplasmic space
M0046872molecular_functionmetal ion binding
M0047806molecular_functioncytochrome-c3 hydrogenase activity
N0008901molecular_functionferredoxin hydrogenase activity
N0016151molecular_functionnickel cation binding
N0016491molecular_functionoxidoreductase activity
N0042597cellular_componentperiplasmic space
N0046872molecular_functionmetal ion binding
N0047806molecular_functioncytochrome-c3 hydrogenase activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI H 551
ChainResidue
HCYS72
HCYS75
HCYS543
HCYS546
HFCO550
HHOH557

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI I 551
ChainResidue
ICYS546
IFCO550
IHOH557
ICYS72
ICYS75
ICYS543

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI J 551
ChainResidue
JCYS72
JCYS75
JCYS543
JCYS546
JFCO550
JHOH557

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI K 551
ChainResidue
KCYS72
KCYS75
KCYS543
KCYS546
KFCO550
KHOH557

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI M 551
ChainResidue
MCYS72
MCYS75
MCYS543
MCYS546
MFCO550
MHOH557

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI N 551
ChainResidue
NCYS72
NCYS75
NCYS543
NCYS546
NFCO550
NHOH557

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG H 553
ChainResidue
HGLU53
HLEU495
HHIS549
HHOH554
HHOH555
HHOH556

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG I 553
ChainResidue
IGLU53
ILEU495
IHIS549
IHOH554
IHOH555
IHOH556

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG J 553
ChainResidue
JGLU53
JLEU495
JHIS549
JHOH554
JHOH555
JHOH556

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG K 553
ChainResidue
KGLU53
KLEU495
KHIS549
KHOH554
KHOH555
KHOH556

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG M 553
ChainResidue
MGLU53
MLEU495
MHIS549
MHOH554
MHOH555
MHOH556

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG N 553
ChainResidue
NGLU53
NLEU495
NHIS549
NHOH554
NHOH555
NHOH556

site_idBC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SF4 A 265
ChainResidue
AHIS184
ACYS187
AARG189
ALEU190
ACYS212
ALEU213
ACYS218

site_idBC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S A 266
ChainResidue
AASN225
ACYS227
APHE232
ACYS245
ALEU246
AGLY247
ACYS248
HLYS225
HGLN230

site_idBC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 A 267
ChainResidue
ACYS17
ACYS20
ATHR113
ACYS114
AGLY146
ACYS147
APRO148
HARG70

site_idBC7
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO H 550
ChainResidue
HALA474
HPRO475
HARG476
HLEU479
HVAL497
HPRO498
HSER499
HCYS546
HNI551
HHOH557
HCYS75
HVAL78
HHIS79

site_idBC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SF4 B 265
ChainResidue
BHIS184
BCYS187
BARG189
BLEU190
BCYS212
BLEU213
BCYS218

site_idBC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S B 266
ChainResidue
BASN225
BCYS227
BPHE232
BTRP237
BCYS245
BLEU246
BCYS248
ILYS225
IGLN230

site_idCC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SF4 B 267
ChainResidue
BGLU16
BCYS17
BCYS20
BGLY112
BTHR113
BCYS114
BGLY146
BCYS147
BPRO148
IARG70

site_idCC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO I 550
ChainResidue
ICYS75
IVAL78
IHIS79
IALA474
IPRO475
IARG476
ILEU479
IVAL497
IPRO498
ISER499
ICYS546
INI551
IHOH557

site_idCC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SF4 C 265
ChainResidue
CHIS184
CCYS187
CARG189
CLEU190
CCYS212
CLEU213
CCYS218

site_idCC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S C 266
ChainResidue
CTHR223
CASN225
CCYS227
CPHE232
CTRP237
CCYS245
CLEU246
CCYS248
JGLN230

site_idCC5
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 C 267
ChainResidue
CGLU16
CCYS17
CCYS20
CGLY112
CTHR113
CCYS114
CGLY146
CCYS147
CPRO148
JARG70
JHIS228

site_idCC6
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO J 550
ChainResidue
JCYS75
JVAL78
JHIS79
JALA474
JPRO475
JARG476
JLEU479
JVAL497
JPRO498
JSER499
JCYS546
JNI551
JHOH557

site_idCC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 D 265
ChainResidue
DHIS184
DCYS187
DARG189
DLEU190
DCYS212
DLEU213
DCYS218
DPRO221

site_idCC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S D 266
ChainResidue
DTHR223
DASN225
DCYS227
DPHE232
DCYS245
DLEU246
DCYS248
KLYS225
KGLN230

site_idCC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 D 267
ChainResidue
DGLU16
DCYS17
DCYS20
DTHR113
DCYS114
DGLY146
DCYS147
KARG70
KHIS228

site_idDC1
Number of Residues12
DetailsBINDING SITE FOR RESIDUE FCO K 550
ChainResidue
KCYS75
KHIS79
KALA474
KPRO475
KARG476
KLEU479
KVAL497
KPRO498
KSER499
KCYS546
KNI551
KHOH557

site_idDC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 F 265
ChainResidue
FHIS184
FCYS187
FARG189
FLEU190
FCYS212
FLEU213
FCYS218
FPRO221

site_idDC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S F 266
ChainResidue
FTHR223
FASN225
FCYS227
FPHE232
FTRP237
FCYS245
FLEU246
FCYS248
MGLN230

site_idDC4
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 F 267
ChainResidue
FGLU16
FCYS17
FCYS20
FGLY112
FTHR113
FCYS114
FGLY146
FCYS147
FPRO148
MARG70
MHIS228

site_idDC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO M 550
ChainResidue
MCYS75
MVAL78
MHIS79
MALA474
MPRO475
MARG476
MLEU479
MVAL497
MPRO498
MSER499
MCYS546
MNI551
MHOH557

site_idDC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SF4 G 265
ChainResidue
GHIS184
GCYS187
GARG189
GLEU190
GCYS212
GLEU213
GCYS218

site_idDC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE F3S G 266
ChainResidue
GASN225
GCYS227
GPRO238
GCYS245
GLEU246
GCYS248
GHOH5277
NLYS225
NGLN230

site_idDC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 G 267
ChainResidue
GGLU16
GCYS17
GCYS20
GTHR113
GCYS114
GCYS147
GPRO148
NARG70
NHIS228

site_idDC9
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO N 550
ChainResidue
NCYS75
NVAL78
NHIS79
NALA474
NPRO475
NARG476
NLEU479
NVAL497
NPRO498
NSER499
NCYS546
NNI551
NHOH557

Functional Information from PROSITE/UniProt
site_idPS00507
Number of Residues26
DetailsNI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEiilkgrdprdaqhftQRaCGVC
ChainResidueDetails
HARG50-CYS75

site_idPS00508
Number of Residues10
DetailsNI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPCIACgv.H
ChainResidueDetails
HPHE540-HIS549

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues66
DetailsBinding site: {}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues24
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
ATHR18
HCYS543
HGLU25

site_idCSA10
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
KCYS543

site_idCSA11
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
MCYS543

site_idCSA12
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
NCYS543

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
ICYS543
IGLU25
BTHR18

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
JCYS543
JGLU25
CTHR18

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
DTHR18
KCYS543
KGLU25

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
FTHR18
MCYS543
MGLU25

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
NCYS543
NGLU25
GTHR18

site_idCSA7
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
HCYS543

site_idCSA8
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
ICYS543

site_idCSA9
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
JCYS543

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PDB entries from 2025-07-09

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