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6Z7R

Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas - structure wtKr1

Functional Information from GO Data
ChainGOidnamespacecontents
A0008901molecular_functionferredoxin hydrogenase activity
A0009375cellular_componentferredoxin hydrogenase complex
A0051536molecular_functioniron-sulfur cluster binding
B0005515molecular_functionprotein binding
B0008901molecular_functionferredoxin hydrogenase activity
B0016151molecular_functionnickel cation binding
B0016491molecular_functionoxidoreductase activity
B0046872molecular_functionmetal ion binding
C0008901molecular_functionferredoxin hydrogenase activity
C0009375cellular_componentferredoxin hydrogenase complex
C0051536molecular_functioniron-sulfur cluster binding
D0005515molecular_functionprotein binding
D0008901molecular_functionferredoxin hydrogenase activity
D0016151molecular_functionnickel cation binding
D0016491molecular_functionoxidoreductase activity
D0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues8
Detailsbinding site for residue SF4 A 301
ChainResidue
AHIS208
ACYS211
ATYR217
ACYS232
AARG233
ACYS238
AGLY240
AVAL260

site_idAC2
Number of Residues9
Detailsbinding site for residue SF4 A 302
ChainResidue
ACYS247
ATRP252
ACYS259
ACYS265
AILE266
AGLY267
ACYS268
BARG182
ATHR243

site_idAC3
Number of Residues11
Detailsbinding site for residue SF4 A 303
ChainResidue
AGLY17
ACYS18
ACYS21
AGLY119
ATHR120
ACYS121
AGLY158
ACYS159
A6ML304
BARG73
BHIS185

site_idAC4
Number of Residues16
Detailsbinding site for residue 6ML A 304
ChainResidue
ACYS18
ATHR19
AGLY20
ACYS21
AGLU77
AGLY78
AGLY119
ATHR120
ACYS121
AGLY158
ACYS159
APRO160
ASF4303
AHOH413
BARG73
BHIS185

site_idAC5
Number of Residues2
Detailsbinding site for residue KR A 306
ChainResidue
AVAL10
AVAL170

site_idAC6
Number of Residues2
Detailsbinding site for residue KR A 307
ChainResidue
APHE73
ALEU174

site_idAC7
Number of Residues2
Detailsbinding site for residue KR A 308
ChainResidue
AVAL36
AKR309

site_idAC8
Number of Residues1
Detailsbinding site for residue KR A 309
ChainResidue
AKR308

site_idAC9
Number of Residues2
Detailsbinding site for residue KR A 311
ChainResidue
ALEU116
AALA173

site_idAD1
Number of Residues1
Detailsbinding site for residue KR A 312
ChainResidue
ALEU26

site_idAD2
Number of Residues3
Detailsbinding site for residue KR A 313
ChainResidue
APRO152
AVAL154
AVAL189

site_idAD3
Number of Residues2
Detailsbinding site for residue KR A 314
ChainResidue
AILE58
AILE91

site_idAD4
Number of Residues1
Detailsbinding site for residue KR A 315
ChainResidue
ALEU172

site_idAD5
Number of Residues12
Detailsbinding site for residue FCO B 501
ChainResidue
BCYS78
BHIS82
BALA420
BPRO421
BARG422
BLEU425
BALA444
BSER445
BSEC489
BCYS492
BNI502
BH2S504

site_idAD6
Number of Residues6
Detailsbinding site for residue NI B 502
ChainResidue
BCSD75
BCYS78
BSEC489
BCYS492
BFCO501
BH2S504

site_idAD7
Number of Residues6
Detailsbinding site for residue FE2 B 503
ChainResidue
BGLU56
BILE441
BHIS495
BHOH602
BHOH610
BHOH611

site_idAD8
Number of Residues6
Detailsbinding site for residue CL B 505
ChainResidue
BCYS78
BTHR80
BALA81
BPHE110
BASN113
BPRO421

site_idAD9
Number of Residues3
Detailsbinding site for residue KR B 506
ChainResidue
BTYR123
BGLY158
BKR507

site_idAE1
Number of Residues3
Detailsbinding site for residue KR B 507
ChainResidue
BPHE122
BILE228
BKR506

site_idAE2
Number of Residues4
Detailsbinding site for residue KR B 508
ChainResidue
BKR509
BGLN128
BVAL131
BTYR162

site_idAE3
Number of Residues4
Detailsbinding site for residue KR B 509
ChainResidue
BPRO134
BPHE139
BTYR162
BKR508

site_idAE4
Number of Residues5
Detailsbinding site for residue KR B 510
ChainResidue
BLEU150
BLEU154
BGLY158
BVAL224
BILE228

site_idAE5
Number of Residues1
Detailsbinding site for residue KR B 511
ChainResidue
BTYR162

site_idAE6
Number of Residues1
Detailsbinding site for residue KR B 512
ChainResidue
BPHE353

site_idAE7
Number of Residues3
Detailsbinding site for residue KR B 513
ChainResidue
BASN337
BPRO339
BTYR384

site_idAE8
Number of Residues9
Detailsbinding site for residue SF4 C 301
ChainResidue
CHIS208
CCYS211
CTYR213
CLEU214
CCYS232
CARG233
CTYR234
CCYS238
CVAL260

site_idAE9
Number of Residues8
Detailsbinding site for residue SF4 C 302
ChainResidue
CTHR243
CCYS247
CTRP252
CCYS259
CCYS265
CILE266
CCYS268
DARG182

site_idAF1
Number of Residues11
Detailsbinding site for residue SF4 C 303
ChainResidue
CGLY17
CCYS18
CCYS21
CGLY119
CTHR120
CCYS121
CGLY158
CCYS159
C6ML304
DARG73
DHIS185

site_idAF2
Number of Residues16
Detailsbinding site for residue 6ML C 304
ChainResidue
CCYS18
CTHR19
CGLY20
CCYS21
CGLU77
CGLY78
CGLY119
CTHR120
CCYS121
CGLY158
CCYS159
CPRO160
CSF4303
CHOH404
DARG73
DHIS185

site_idAF3
Number of Residues4
Detailsbinding site for residue KR C 306
ChainResidue
CVAL10
CLEU116
CVAL170
CKR311

site_idAF4
Number of Residues2
Detailsbinding site for residue KR C 307
ChainResidue
CPHE73
CLEU174

site_idAF5
Number of Residues1
Detailsbinding site for residue KR C 308
ChainResidue
CALA173

site_idAF6
Number of Residues1
Detailsbinding site for residue KR C 309
ChainResidue
CLEU26

site_idAF7
Number of Residues1
Detailsbinding site for residue KR C 310
ChainResidue
CKR311

site_idAF8
Number of Residues3
Detailsbinding site for residue KR C 311
ChainResidue
CKR306
CKR310
CKR312

site_idAF9
Number of Residues4
Detailsbinding site for residue KR C 312
ChainResidue
CVAL75
CLEU116
CILE166
CKR311

site_idAG1
Number of Residues2
Detailsbinding site for residue KR C 314
ChainResidue
CPRO152
CVAL154

site_idAG2
Number of Residues2
Detailsbinding site for residue KR C 315
ChainResidue
CLEU172
CVAL192

site_idAG3
Number of Residues2
Detailsbinding site for residue KR C 316
ChainResidue
CILE58
CMET61

site_idAG4
Number of Residues5
Detailsbinding site for residue KR C 317
ChainResidue
CILE127
CPHE273
DGLN69
DILE70
DARG73

site_idAG5
Number of Residues11
Detailsbinding site for residue FCO D 501
ChainResidue
DCYS78
DALA420
DPRO421
DARG422
DLEU425
DALA444
DSER445
DSEC489
DCYS492
DNI502
DH2S504

site_idAG6
Number of Residues6
Detailsbinding site for residue NI D 502
ChainResidue
DCSD75
DCYS78
DSEC489
DCYS492
DFCO501
DH2S504

site_idAG7
Number of Residues5
Detailsbinding site for residue FE2 D 503
ChainResidue
DGLU56
DILE441
DHIS495
DHOH603
DHOH604

site_idAG8
Number of Residues6
Detailsbinding site for residue CL D 505
ChainResidue
DCYS78
DTHR80
DALA81
DPHE110
DASN113
DPRO421

site_idAG9
Number of Residues5
Detailsbinding site for residue KR D 506
ChainResidue
DPHE122
DTYR123
DALA127
DGLY158
DILE228

site_idAH1
Number of Residues2
Detailsbinding site for residue KR D 507
ChainResidue
DTYR162
DKR510

site_idAH2
Number of Residues3
Detailsbinding site for residue KR D 508
ChainResidue
DLEU426
DVAL442
DTRP447

site_idAH3
Number of Residues1
Detailsbinding site for residue KR D 509
ChainResidue
DTYR162

site_idAH4
Number of Residues4
Detailsbinding site for residue KR D 510
ChainResidue
DPRO134
DPHE139
DTYR162
DKR507

site_idAH5
Number of Residues5
Detailsbinding site for residue KR D 511
ChainResidue
DLEU150
DLEU154
DGLY158
DVAL224
DILE228

site_idAH6
Number of Residues1
Detailsbinding site for residue KR D 512
ChainResidue
DPHE236

site_idAH7
Number of Residues13
Detailsbinding site for residues H2S B 504 and SEC B 489
ChainResidue
BGLU28
BCSD75
BCYS78
BARG422
BSER445
BASP487
BPRO488
BLEU490
BGLY491
BCYS492
BALA493
BFCO501
BNI502

site_idAH8
Number of Residues13
Detailsbinding site for residues H2S B 504 and SEC B 489
ChainResidue
BGLU28
BCSD75
BCYS78
BARG422
BSER445
BASP487
BPRO488
BLEU490
BGLY491
BCYS492
BALA493
BFCO501
BNI502

site_idAH9
Number of Residues12
Detailsbinding site for residues H2S D 504 and SEC D 489
ChainResidue
DGLU28
DCSD75
DCYS78
DARG422
DSER445
DPRO488
DLEU490
DGLY491
DCYS492
DALA493
DFCO501
DNI502

site_idAI1
Number of Residues12
Detailsbinding site for residues H2S D 504 and SEC D 489
ChainResidue
DGLU28
DCSD75
DCYS78
DARG422
DSER445
DPRO488
DLEU490
DGLY491
DCYS492
DALA493
DFCO501
DNI502

Functional Information from PROSITE/UniProt
site_idPS00507
Number of Residues26
DetailsNI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGFEtilrgrdprdasqivQRiCGVC
ChainResidueDetails
BARG53-CYS78

site_idPS00508
Number of Residues10
DetailsNI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPULGCav.H
ChainResidueDetails
BPHE486-HIS495

226707

PDB entries from 2024-10-30

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