Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

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 Residues24
DetailsBINDING: BINDING => ECO:0000255
ChainResidueDetails
HCYS72
JCYS75
JCYS543
JCYS546
KCYS72
KCYS75
KCYS543
KCYS546
MCYS72
MCYS75
MCYS543
HCYS75
MCYS546
NCYS72
NCYS75
NCYS543
NCYS546
CCYS114
CCYS147
CHIS184
CCYS187
CCYS212
HCYS543
CCYS218
CCYS227
CCYS245
CCYS248
DCYS17
DCYS20
DCYS114
DCYS147
DHIS184
DCYS187
HCYS546
DCYS212
DCYS218
DCYS227
DCYS245
DCYS248
FCYS17
FCYS20
FCYS114
FCYS147
FHIS184
ICYS72
FCYS187
FCYS212
FCYS218
FCYS227
FCYS245
FCYS248
GCYS17
GCYS20
GCYS114
GCYS147
ICYS75
GHIS184
GCYS187
GCYS212
GCYS218
GCYS227
GCYS245
GCYS248
ICYS543
ICYS546
JCYS72

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

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

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

219140

PDB entries from 2024-05-01

PDB statisticsPDBj update infoContact PDBjnumon