Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1YQW

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009055	molecular_function	electron transfer activity
A	0009061	biological_process	anaerobic respiration
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0042597	cellular_component	periplasmic space
A	0044569	cellular_component	[Ni-Fe] hydrogenase complex
A	0046872	molecular_function	metal ion binding
A	0047806	molecular_function	cytochrome-c3 hydrogenase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051538	molecular_function	3 iron, 4 sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0009055	molecular_function	electron transfer activity
B	0009061	biological_process	anaerobic respiration
B	0009375	cellular_component	ferredoxin hydrogenase complex
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0042597	cellular_component	periplasmic space
B	0044569	cellular_component	[Ni-Fe] hydrogenase complex
B	0046872	molecular_function	metal ion binding
B	0047806	molecular_function	cytochrome-c3 hydrogenase activity
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051538	molecular_function	3 iron, 4 sulfur cluster binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009055	molecular_function	electron transfer activity
C	0009061	biological_process	anaerobic respiration
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0042597	cellular_component	periplasmic space
C	0044569	cellular_component	[Ni-Fe] hydrogenase complex
C	0046872	molecular_function	metal ion binding
C	0047806	molecular_function	cytochrome-c3 hydrogenase activity
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051538	molecular_function	3 iron, 4 sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
Q	0008901	molecular_function	ferredoxin hydrogenase activity
Q	0016151	molecular_function	nickel cation binding
Q	0016491	molecular_function	oxidoreductase activity
Q	0042597	cellular_component	periplasmic space
Q	0046872	molecular_function	metal ion binding
Q	0047806	molecular_function	cytochrome-c3 hydrogenase activity
R	0008901	molecular_function	ferredoxin hydrogenase activity
R	0016151	molecular_function	nickel cation binding
R	0016491	molecular_function	oxidoreductase activity
R	0042597	cellular_component	periplasmic space
R	0046872	molecular_function	metal ion binding
R	0047806	molecular_function	cytochrome-c3 hydrogenase activity
S	0008901	molecular_function	ferredoxin hydrogenase activity
S	0016151	molecular_function	nickel cation binding
S	0016491	molecular_function	oxidoreductase activity
S	0042597	cellular_component	periplasmic space
S	0046872	molecular_function	metal ion binding
S	0047806	molecular_function	cytochrome-c3 hydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NI Q 551

Chain	Residue
Q	CYS72
Q	CYS75
Q	CYS543
Q	CYS546
Q	FCO550
Q	PER552
Q	HOH564

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 Q 553

Chain	Residue
Q	GLU53
Q	LEU495
Q	HIS549
Q	HOH561
Q	HOH562
Q	HOH563

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NI R 551

Chain	Residue
R	CYS72
R	CYS75
R	CYS543
R	CYS546
R	FCO550
R	PER552
R	HOH557

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 R 553

Chain	Residue
R	GLU53
R	LEU495
R	HIS549
R	HOH554
R	HOH555
R	HOH556

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NI S 551

Chain	Residue
S	CYS72
S	CYS75
S	CYS543
S	CYS546
S	FCO550
S	PER552
S	HOH557

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 S 553

Chain	Residue
S	GLU53
S	LEU495
S	HIS549
S	HOH554
S	HOH555
S	HOH556

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BCT Q 554

Chain	Residue
Q	GLU465
Q	SER466
Q	LYS467
Q	ARG484
Q	HOH1028

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG Q 555

Chain	Residue
A	HOH360
C	HOH269
C	HOH270
Q	ASN181
Q	HOH1026
Q	HOH1031

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG Q 556

Chain	Residue
Q	ASP88
Q	ILE95
Q	ARG103
Q	HOH699
Q	HOH1025
Q	HOH1027

site_id	AS1
Number of Residues	6
Details	NI-FE ACTIVE SITE IN MOLECULE 1 SITE

Chain	Residue
Q	CYS72
Q	CYS75
Q	CYS543
Q	CYS546
Q	FCO550
Q	NI551

site_id	AS2
Number of Residues	6
Details	NI-FE ACTIVE SITE IN MOLECULE 2 SITE

Chain	Residue
R	CYS72
R	CYS75
R	CYS543
R	CYS546
R	FCO550
R	NI551

site_id	AS3
Number of Residues	6
Details	NI-FE ACTIVE SITE IN MOLECULE 3 SITE

Chain	Residue
S	CYS72
S	CYS75
S	CYS543
S	CYS546
S	FCO550
S	NI551

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG R 1308

Chain	Residue
B	HOH1626
R	ASN181
R	HOH1628
R	HOH1676

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 A 265

Chain	Residue
A	HIS184
A	CYS187
A	ARG189
A	LEU190
A	CYS212
A	LEU213
A	CYS218

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S A 266

Chain	Residue
A	ASN225
A	CYS227
A	PHE232
A	TRP237
A	CYS245
A	LEU246
A	CYS248
Q	GLN230

site_id	BC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SF4 A 267

Chain	Residue
A	GLU16
A	CYS17
A	CYS20
A	GLY112
A	THR113
A	CYS114
A	GLY146
A	CYS147
A	PRO148
Q	ARG70
Q	HIS228

site_id	BC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE FCO Q 550

Chain	Residue
Q	CYS75
Q	VAL78
Q	HIS79
Q	ALA474
Q	PRO475
Q	ARG476
Q	LEU479
Q	VAL497
Q	PRO498
Q	ALA499
Q	CYS546
Q	NI551
Q	PER552
Q	HOH583

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PER Q 552

Chain	Residue
Q	CYS72
Q	CYS75
Q	ARG476
Q	CYS543
Q	CYS546
Q	FCO550
Q	NI551
Q	HOH564

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 B 265

Chain	Residue
B	HIS184
B	CYS187
B	ARG189
B	LEU190
B	CYS212
B	LEU213
B	CYS218

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE F3S B 266

Chain	Residue
B	ASN225
B	CYS227
B	PHE232
B	CYS245
B	LEU246
B	CYS248
R	GLN230

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 B 267

Chain	Residue
B	GLU16
B	CYS17
B	CYS20
B	THR113
B	CYS114
B	GLY146
B	CYS147
B	PRO148
R	ARG70
R	HIS228

site_id	CC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE FCO R 550

Chain	Residue
R	CYS75
R	VAL78
R	HIS79
R	ALA474
R	PRO475
R	ARG476
R	LEU479
R	VAL497
R	PRO498
R	ALA499
R	CYS546
R	NI551
R	PER552
R	HOH1690

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PER R 552

Chain	Residue
R	CYS75
R	ARG476
R	CYS543
R	CYS546
R	FCO550
R	NI551

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 C 265

Chain	Residue
C	HIS184
C	CYS187
C	ARG189
C	LEU190
C	CYS212
C	LEU213
C	CYS218

site_id	CC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S C 266

Chain	Residue
C	THR223
C	ASN225
C	CYS227
C	PHE232
C	TRP237
C	CYS245
C	LEU246
C	CYS248
S	GLN230

site_id	CC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 C 267

Chain	Residue
C	CYS17
C	CYS20
C	THR113
C	CYS114
C	GLY146
C	CYS147
C	PRO148
S	ARG70
S	HIS228

site_id	CC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE FCO S 550

Chain	Residue
S	CYS75
S	VAL78
S	HIS79
S	ALA474
S	PRO475
S	ARG476
S	LEU479
S	VAL497
S	PRO498
S	ALA499
S	CYS546
S	NI551
S	PER552
S	HOH2477

site_id	CC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PER S 552

Chain	Residue
S	CYS72
S	CYS75
S	ARG476
S	CYS543
S	CYS546
S	FCO550
S	NI551
S	HOH557

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 268

Chain	Residue
A	ASP168
A	LEU169
A	LYS176
A	GOL269

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 269

Chain	Residue
A	LYS140
A	LEU169
A	ASP170
A	GOL268

site_id	CT1
Number of Residues	7
Details	C-TERMINAL METAL SITE IN MOLECULE 1 SITE

Chain	Residue
Q	GLU53
Q	LEU495
Q	HIS549
Q	FE2553
Q	HOH561
Q	HOH562
Q	HOH563

site_id	CT2
Number of Residues	7
Details	C-TERMINAL METAL SITE IN MOLECULE 2 SITE

Chain	Residue
R	GLU53
R	LEU495
R	HIS549
R	FE2553
R	HOH554
R	HOH555
R	HOH556

site_id	CT3
Number of Residues	7
Details	C-TERMINAL METAL SITE IN MOLECULE 3

Chain	Residue
S	GLU53
S	LEU495
S	HIS549
S	FE2553
S	HOH554
S	HOH555
S	HOH556

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 270

Chain	Residue
A	ARG6
A	LEU37
A	ASP38
Q	PHE170
Q	HOH745

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL Q 557

Chain	Residue
Q	ARG100
Q	ASN104
Q	PHE295
Q	ALA296
Q	THR297
Q	GLU445
Q	HOH665
Q	HOH1023
Q	HOH1030

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL Q 558

Chain	Residue
A	ALA55
C	PHE198
Q	ASN181
Q	ALA182
Q	LEU185
Q	ARG529
Q	HOH872
Q	HOH1031

site_id	DC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL Q 559

Chain	Residue
Q	GLY281
Q	GLY282
Q	ILE283
Q	GLY284
Q	GLY285
Q	ARG319
Q	HIS419
Q	HOH974
Q	HOH1029

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL Q 560

Chain	Residue
Q	LYS245
Q	LYS337
Q	TYR338
Q	ASP366

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL R 1301

Chain	Residue
R	ASN181
R	ALA182
R	TYR183
R	LEU185
R	ARG529
R	HOH1676

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL R 1302

Chain	Residue
B	ALA136
B	LEU137
B	GLY138
R	GLY409
R	LYS410
R	HOH1613

site_id	DC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL R 1303

Chain	Residue
R	ARG100
R	ASN104
R	PHE295
R	ALA296
R	THR297
R	TRP442
R	GLU445
R	HOH1438
R	HOH1578
R	HOH1632

site_id	DC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL R 1304

Chain	Residue
R	GLY281
R	GLY282
R	ILE283
R	GLY284
R	GLY285
R	ARG319
R	HIS419
R	HOH1576

site_id	EC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL R 1305

Chain	Residue
R	THR286
R	SER287
R	ASN288
R	ALA380
R	PRO514
R	HOH1373
R	HOH1415

site_id	EC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL R 1306

Chain	Residue
R	ARG152
R	PRO153
R	ASN155
R	SER156
R	HOH1444
R	HOH1472
S	ALA451
S	GOL2302

site_id	EC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL R 1307

Chain	Residue
R	GLU465
R	LYS467
R	ARG484
R	HOH1646
R	HOH1721

site_id	EC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL S 2301

Chain	Residue
S	ARG100
S	ASN104
S	PHE295
S	ALA296
S	THR297
S	GLU445
S	HOH2405
S	HOH2581
S	HOH2593

site_id	EC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL S 2302

Chain	Residue
R	GOL1306
S	GLY450
S	ALA451
S	LYS452
S	ASP453
S	ASN454
S	HOH2544

site_id	EC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL S 2303

Chain	Residue
C	VAL235
S	SER217
S	ASN250
S	HOH2524

site_id	FD1
Number of Residues	5
Details	DISTAL [4FE-4S] CLUSTER IN MOLECULE 1 SITE

Chain	Residue
A	HIS184
A	CYS187
A	CYS212
A	CYS218
A	SF4265

site_id	FD2
Number of Residues	5
Details	DISTAL [4FE-4S] CLUSTER IN MOLECULE 2 SITE

Chain	Residue
B	HIS184
B	CYS187
B	CYS212
B	CYS218
B	SF4265

site_id	FD3
Number of Residues	5
Details	DISTAL [4FE-4S] CLUSTER IN MOLECULE 3 SITE

Chain	Residue
C	HIS184
C	CYS187
C	CYS212
C	CYS218
C	SF4265

site_id	FM1
Number of Residues	4
Details	[3FE-4S] CLUSTER IN MOLECULE 1 SITE

Chain	Residue
A	CYS227
A	CYS245
A	CYS248
A	F3S266

site_id	FM2
Number of Residues	4
Details	[3FE-4S] CLUSTER IN MOLECULE 2 SITE

Chain	Residue
B	CYS227
B	CYS245
B	CYS248
B	F3S266

site_id	FM3
Number of Residues	4
Details	[3FE-4S] CLUSTER IN MOLECULE 3 SITE

Chain	Residue
C	CYS227
C	CYS245
C	CYS248
C	F3S266

site_id	FP1
Number of Residues	5
Details	PROXIMAL [4FE-4S] CLUSTER IN MOLECULE 1 SITE

Chain	Residue
A	CYS17
A	CYS20
A	CYS114
A	CYS147
A	SF4267

site_id	FP2
Number of Residues	5
Details	PROXIMAL [4FE-4S] CLUSTER IN MOLECULE 2 SITE

Chain	Residue
B	CYS17
B	CYS20
B	CYS114
B	CYS147
B	SF4267

site_id	FP3
Number of Residues	5
Details	PROXIMAL [4FE-4S] CLUSTER IN MOLECULE 3 SITE

Chain	Residue
C	CYS17
C	CYS20
C	CYS114
C	CYS147
C	SF4267

site_id	PO1
Number of Residues	3
Details	ACTIVE SITE BOUND PEROXIDE IN MOLECULE 1 SITE

Chain	Residue
Q	NI551
Q	FCO550
Q	PER552

site_id	PO2
Number of Residues	3
Details	ACTIVE SITE BOUND PEROXIDE IN MOLECULE 2 SITE

Chain	Residue
R	NI551
R	FCO550
R	PER552

site_id	PO3
Number of Residues	3
Details	ACTIVE SITE BOUND PEROXIDE IN MOLECULE 3 SITE

Chain	Residue
S	NI551
S	FCO550
S	PER552

site_id	SO1
Number of Residues	3
Details	NIFE-BOUND SULPHENIC ACID IN MOLECULE 1 SITE

Chain	Residue
Q	CYS75
Q	NI551
Q	HOH564

site_id	SO2
Number of Residues	3
Details	NIFE-BOUND SULPHENIC ACID IN MOLECULE 2 SITE

Chain	Residue
R	CYS75
R	NI551
R	HOH557

site_id	SO3
Number of Residues	3
Details	NIFE-BOUND SULPHENIC ACID IN MOLECULE 3 SITE

Chain	Residue
S	CYS75
S	NI551
S	HOH557

Functional Information from PROSITE/UniProt

site_id	PS00507
Number of Residues	26
Details	NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEiilkgrdprdaqhftQRaCGVC

Chain	Residue	Details
Q	ARG50-CYS75

site_id	PS00508
Number of Residues	10
Details	NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPCIACgv.H

Chain	Residue	Details
Q	PHE540-HIS549

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	33
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
A	THR18
Q	CYS543
Q	GLU25

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
R	CYS543
R	GLU25
B	THR18

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
S	CYS543
S	GLU25
C	THR18

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
Q	CYS543

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
R	CYS543

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
S	CYS543

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)