Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0005515	molecular_function	protein binding
A	0005886	cellular_component	plasma membrane
A	0006113	biological_process	fermentation
A	0009055	molecular_function	electron transfer activity
A	0009061	biological_process	anaerobic respiration
A	0009267	biological_process	cellular response to starvation
A	0016020	cellular_component	membrane
A	0019645	biological_process	anaerobic electron transport chain
A	0020037	molecular_function	heme binding
A	0022904	biological_process	respiratory electron transport chain
A	0033748	molecular_function	hydrogenase (acceptor) activity
A	0044569	cellular_component	[Ni-Fe] hydrogenase complex
A	0046872	molecular_function	metal ion binding
A	0098567	cellular_component	periplasmic side of plasma membrane
A	1902421	biological_process	hydrogen metabolic process
B	0005506	molecular_function	iron ion binding
B	0005515	molecular_function	protein binding
B	0005886	cellular_component	plasma membrane
B	0006113	biological_process	fermentation
B	0009055	molecular_function	electron transfer activity
B	0009061	biological_process	anaerobic respiration
B	0009267	biological_process	cellular response to starvation
B	0016020	cellular_component	membrane
B	0019645	biological_process	anaerobic electron transport chain
B	0020037	molecular_function	heme binding
B	0022904	biological_process	respiratory electron transport chain
B	0033748	molecular_function	hydrogenase (acceptor) activity
B	0044569	cellular_component	[Ni-Fe] hydrogenase complex
B	0046872	molecular_function	metal ion binding
B	0098567	cellular_component	periplasmic side of plasma membrane
B	1902421	biological_process	hydrogen metabolic process
J	0005515	molecular_function	protein binding
J	0005886	cellular_component	plasma membrane
J	0006113	biological_process	fermentation
J	0008901	molecular_function	ferredoxin hydrogenase activity
J	0009055	molecular_function	electron transfer activity
J	0009061	biological_process	anaerobic respiration
J	0009267	biological_process	cellular response to starvation
J	0016020	cellular_component	membrane
J	0016151	molecular_function	nickel cation binding
J	0016491	molecular_function	oxidoreductase activity
J	0019645	biological_process	anaerobic electron transport chain
J	0030288	cellular_component	outer membrane-bounded periplasmic space
J	0033748	molecular_function	hydrogenase (acceptor) activity
J	0044569	cellular_component	[Ni-Fe] hydrogenase complex
J	0046872	molecular_function	metal ion binding
J	0098567	cellular_component	periplasmic side of plasma membrane
J	1902421	biological_process	hydrogen metabolic process
K	0005515	molecular_function	protein binding
K	0005886	cellular_component	plasma membrane
K	0006113	biological_process	fermentation
K	0008901	molecular_function	ferredoxin hydrogenase activity
K	0009055	molecular_function	electron transfer activity
K	0009061	biological_process	anaerobic respiration
K	0009267	biological_process	cellular response to starvation
K	0016020	cellular_component	membrane
K	0016151	molecular_function	nickel cation binding
K	0016491	molecular_function	oxidoreductase activity
K	0019645	biological_process	anaerobic electron transport chain
K	0030288	cellular_component	outer membrane-bounded periplasmic space
K	0033748	molecular_function	hydrogenase (acceptor) activity
K	0044569	cellular_component	[Ni-Fe] hydrogenase complex
K	0046872	molecular_function	metal ion binding
K	0098567	cellular_component	periplasmic side of plasma membrane
K	1902421	biological_process	hydrogen metabolic process
L	0005515	molecular_function	protein binding
L	0005886	cellular_component	plasma membrane
L	0006113	biological_process	fermentation
L	0008901	molecular_function	ferredoxin hydrogenase activity
L	0009055	molecular_function	electron transfer activity
L	0009061	biological_process	anaerobic respiration
L	0009267	biological_process	cellular response to starvation
L	0016020	cellular_component	membrane
L	0016151	molecular_function	nickel cation binding
L	0016491	molecular_function	oxidoreductase activity
L	0019645	biological_process	anaerobic electron transport chain
L	0030288	cellular_component	outer membrane-bounded periplasmic space
L	0033748	molecular_function	hydrogenase (acceptor) activity
L	0044569	cellular_component	[Ni-Fe] hydrogenase complex
L	0046872	molecular_function	metal ion binding
L	0098567	cellular_component	periplasmic side of plasma membrane
L	1902421	biological_process	hydrogen metabolic process
M	0005515	molecular_function	protein binding
M	0005886	cellular_component	plasma membrane
M	0006113	biological_process	fermentation
M	0008901	molecular_function	ferredoxin hydrogenase activity
M	0009055	molecular_function	electron transfer activity
M	0009061	biological_process	anaerobic respiration
M	0009267	biological_process	cellular response to starvation
M	0016020	cellular_component	membrane
M	0016151	molecular_function	nickel cation binding
M	0016491	molecular_function	oxidoreductase activity
M	0019645	biological_process	anaerobic electron transport chain
M	0030288	cellular_component	outer membrane-bounded periplasmic space
M	0033748	molecular_function	hydrogenase (acceptor) activity
M	0044569	cellular_component	[Ni-Fe] hydrogenase complex
M	0046872	molecular_function	metal ion binding
M	0098567	cellular_component	periplasmic side of plasma membrane
M	1902421	biological_process	hydrogen metabolic process
Q	0005515	molecular_function	protein binding
Q	0005886	cellular_component	plasma membrane
Q	0006113	biological_process	fermentation
Q	0008901	molecular_function	ferredoxin hydrogenase activity
Q	0009055	molecular_function	electron transfer activity
Q	0009061	biological_process	anaerobic respiration
Q	0009267	biological_process	cellular response to starvation
Q	0009375	cellular_component	ferredoxin hydrogenase complex
Q	0016020	cellular_component	membrane
Q	0016491	molecular_function	oxidoreductase activity
Q	0019645	biological_process	anaerobic electron transport chain
Q	0033748	molecular_function	hydrogenase (acceptor) activity
Q	0044569	cellular_component	[Ni-Fe] hydrogenase complex
Q	0046872	molecular_function	metal ion binding
Q	0051536	molecular_function	iron-sulfur cluster binding
Q	0051538	molecular_function	3 iron, 4 sulfur cluster binding
Q	0051539	molecular_function	4 iron, 4 sulfur cluster binding
Q	0098567	cellular_component	periplasmic side of plasma membrane
Q	1902421	biological_process	hydrogen metabolic process
R	0005515	molecular_function	protein binding
R	0005886	cellular_component	plasma membrane
R	0006113	biological_process	fermentation
R	0008901	molecular_function	ferredoxin hydrogenase activity
R	0009055	molecular_function	electron transfer activity
R	0009061	biological_process	anaerobic respiration
R	0009267	biological_process	cellular response to starvation
R	0009375	cellular_component	ferredoxin hydrogenase complex
R	0016020	cellular_component	membrane
R	0016491	molecular_function	oxidoreductase activity
R	0019645	biological_process	anaerobic electron transport chain
R	0033748	molecular_function	hydrogenase (acceptor) activity
R	0044569	cellular_component	[Ni-Fe] hydrogenase complex
R	0046872	molecular_function	metal ion binding
R	0051536	molecular_function	iron-sulfur cluster binding
R	0051538	molecular_function	3 iron, 4 sulfur cluster binding
R	0051539	molecular_function	4 iron, 4 sulfur cluster binding
R	0098567	cellular_component	periplasmic side of plasma membrane
R	1902421	biological_process	hydrogen metabolic process
S	0005515	molecular_function	protein binding
S	0005886	cellular_component	plasma membrane
S	0006113	biological_process	fermentation
S	0008901	molecular_function	ferredoxin hydrogenase activity
S	0009055	molecular_function	electron transfer activity
S	0009061	biological_process	anaerobic respiration
S	0009267	biological_process	cellular response to starvation
S	0009375	cellular_component	ferredoxin hydrogenase complex
S	0016020	cellular_component	membrane
S	0016491	molecular_function	oxidoreductase activity
S	0019645	biological_process	anaerobic electron transport chain
S	0033748	molecular_function	hydrogenase (acceptor) activity
S	0044569	cellular_component	[Ni-Fe] hydrogenase complex
S	0046872	molecular_function	metal ion binding
S	0051536	molecular_function	iron-sulfur cluster binding
S	0051538	molecular_function	3 iron, 4 sulfur cluster binding
S	0051539	molecular_function	4 iron, 4 sulfur cluster binding
S	0098567	cellular_component	periplasmic side of plasma membrane
S	1902421	biological_process	hydrogen metabolic process
T	0005515	molecular_function	protein binding
T	0005886	cellular_component	plasma membrane
T	0006113	biological_process	fermentation
T	0008901	molecular_function	ferredoxin hydrogenase activity
T	0009055	molecular_function	electron transfer activity
T	0009061	biological_process	anaerobic respiration
T	0009267	biological_process	cellular response to starvation
T	0009375	cellular_component	ferredoxin hydrogenase complex
T	0016020	cellular_component	membrane
T	0016491	molecular_function	oxidoreductase activity
T	0019645	biological_process	anaerobic electron transport chain
T	0033748	molecular_function	hydrogenase (acceptor) activity
T	0044569	cellular_component	[Ni-Fe] hydrogenase complex
T	0046872	molecular_function	metal ion binding
T	0051536	molecular_function	iron-sulfur cluster binding
T	0051538	molecular_function	3 iron, 4 sulfur cluster binding
T	0051539	molecular_function	4 iron, 4 sulfur cluster binding
T	0098567	cellular_component	periplasmic side of plasma membrane
T	1902421	biological_process	hydrogen metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 S 401

Chain	Residue
S	HIS187
S	ILE243
S	CYS190
S	ARG192
S	ARG193
S	CYS215
S	LEU216
S	TYR217
S	CYS221
S	PRO224

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 S 402

Chain	Residue
S	THR226
S	CYS230
S	TRP235
S	CYS242
S	CYS249
S	LEU250
S	CYS252

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F4S S 403

Chain	Residue
L	HIS229
S	CYS17
S	THR18
S	CYS19
S	CYS20
S	THR114
S	CYS115
S	CYS120
S	CYS149

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL S 404

Chain	Residue
S	TRP118
S	GLY119
S	CYS120
S	GLY256

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL S 405

Chain	Residue
M	LEU259
S	HIS29
S	ASP237

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE FCO L 601

Chain	Residue
L	CYS79
L	VAL82
L	HIS83
L	ALA507
L	PRO508
L	ARG509
L	LEU512
L	VAL530
L	PRO531
L	THR532
L	CYS579
L	NI602

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI L 602

Chain	Residue
L	CYS76
L	CYS79
L	CYS576
L	CYS579
L	FCO601

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG L 603

Chain	Residue
L	GLU57
L	CYS528
L	HIS582
L	HOH701
L	HOH702
L	HOH703

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL L 604

Chain	Residue
L	PHE212
L	ARG266

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 T 401

Chain	Residue
T	HIS187
T	CYS190
T	ARG192
T	ARG193
T	CYS215
T	LEU216
T	CYS221
T	PRO224
T	ILE243

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 T 402

Chain	Residue
T	THR226
T	CYS230
T	TRP235
T	CYS242
T	CYS249
T	LEU250
T	CYS252

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE F4S T 403

Chain	Residue
T	CYS17
T	THR18
T	CYS19
T	CYS20
T	CYS115
T	CYS120
T	CYS149

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LMT T 404

Chain	Residue
T	THR281
T	LEU284
T	THR285

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL M 601

Chain	Residue
M	VAL78
M	HIS117
T	GLU22
T	ARG26

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO M 602

Chain	Residue
M	CYS579
M	NI603
M	CYS79
M	VAL82
M	HIS83
M	ALA507
M	PRO508
M	ARG509
M	LEU512
M	VAL530
M	PRO531
M	THR532
M	CYS576

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI M 603

Chain	Residue
M	CYS76
M	CYS79
M	CYS576
M	CYS579
M	FCO602

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG M 604

Chain	Residue
M	GLU57
M	CYS528
M	HIS582
M	HOH701
M	HOH702
M	HOH703

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL M 605

Chain	Residue
M	ILE243
M	ASN253
M	MET254
S	MET180

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 Q 401

Chain	Residue
Q	HIS187
Q	CYS190
Q	ARG192
Q	ARG193
Q	CYS215
Q	LEU216
Q	TYR217
Q	CYS221
Q	PRO224
Q	ILE243

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 Q 402

Chain	Residue
Q	THR226
Q	CYS230
Q	TRP235
Q	CYS242
Q	CYS249
Q	LEU250
Q	CYS252

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F4S Q 403

Chain	Residue
Q	CYS17
Q	THR18
Q	CYS19
Q	CYS20
Q	THR114
Q	CYS115
Q	CYS120
Q	CYS149

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL Q 404

Chain	Residue
Q	TRP118
Q	CYS120
Q	GLY256

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL Q 405

Chain	Residue
K	LEU259
Q	HIS29
Q	ASP237

site_id	CC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE FCO J 601

Chain	Residue
J	CYS79
J	VAL82
J	HIS83
J	ALA507
J	PRO508
J	ARG509
J	LEU512
J	VAL530
J	PRO531
J	THR532
J	CYS579
J	NI602

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI J 602

Chain	Residue
J	CYS76
J	CYS79
J	CYS576
J	CYS579
J	FCO601

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG J 603

Chain	Residue
J	GLU57
J	CYS528
J	HIS582
J	HOH701
J	HOH702
J	HOH703

site_id	CC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL J 604

Chain	Residue
J	PHE212
J	ARG266

site_id	DC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 R 401

Chain	Residue
R	HIS187
R	CYS190
R	ARG192
R	ARG193
R	PHE196
R	CYS215
R	LEU216
R	TYR217
R	CYS221
R	ILE243

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 R 402

Chain	Residue
R	THR226
R	CYS230
R	TRP235
R	CYS242
R	CYS249
R	LEU250
R	CYS252

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F4S R 403

Chain	Residue
R	CYS17
R	THR18
R	CYS19
R	CYS20
R	THR114
R	CYS115
R	CYS120
R	CYS149

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LMT R 404

Chain	Residue
R	THR281
R	LEU284
R	THR285

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL K 601

Chain	Residue
K	GLY77
K	VAL78
K	THR80
K	HIS117
R	GLU22
R	ARG26

site_id	DC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO K 602

Chain	Residue
K	CYS79
K	VAL82
K	HIS83
K	ALA507
K	PRO508
K	ARG509
K	LEU512
K	VAL530
K	PRO531
K	THR532
K	CYS576
K	CYS579
K	NI603

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI K 603

Chain	Residue
K	CYS76
K	CYS79
K	CYS576
K	CYS579
K	FCO602

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG K 604

Chain	Residue
K	GLU57
K	CYS528
K	HIS582
K	HOH701
K	HOH702
K	HOH703

site_id	DC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL K 605

Chain	Residue
K	ILE243
K	ASN253
K	MET254
Q	MET180

site_id	EC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE HEM A 301

Chain	Residue
A	LEU32
A	MET33
A	GLY36
A	TYR37
A	ILE39
A	GLY40
A	ARG60
A	HIS63
A	PHE64
A	THR71
A	MET143
A	GLY147
A	PHE148
A	TYR151
A	HIS181
A	HIS184
A	ARG185

site_id	EC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT A 302

Chain	Residue
A	PRO42
A	LEU43
A	PRO44
T	GLN203
T	LYS218

site_id	EC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE HEM B 301

Chain	Residue
B	LEU32
B	MET33
B	GLY36
B	GLY40
B	ARG60
B	HIS63
B	PHE64
B	MET143
B	GLY147
B	PHE148
B	TYR151
B	HIS181
B	HIS184
B	ARG185
B	ILE191

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT B 302

Chain	Residue
B	PRO42
B	LEU43
B	PRO44
R	GLN203
R	LYS218

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
L	ARG54-CYS79

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

Chain	Residue	Details
L	PHE573-HIS582

site_id	PS00882
Number of Residues	18
Details	NI_HGENASE_CYTB_1 Nickel-dependent hydrogenases b-type cytochrome subunit signature 1. RIwHWLtvLCMavLmVTG

Chain	Residue	Details
A	ARG19-GLY36

site_id	PS00883
Number of Residues	18
Details	NI_HGENASE_CYTB_2 Nickel-dependent hydrogenases b-type cytochrome subunit signature 2. HSWHRLgmWlIgaFvigH

Chain	Residue	Details
A	HIS181-HIS198

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	188
Details	TOPO_DOM: Cytoplasmic => ECO:0000255

Chain	Residue	Details
A	MET1-ARG19
J	CYS79
J	CYS576
J	CYS579
K	CYS76
K	CYS79
K	CYS576
K	CYS579
A	ASN85-GLN130
A	ARG204-SER235
B	MET1-ARG19
B	ASN85-GLN130
B	ARG204-SER235
M	CYS576
M	CYS579
J	CYS76

site_id	SWS_FT_FI2
Number of Residues	154
Details	TRANSMEM: Helical => ECO:0000255

Chain	Residue	Details
A	ILE20-GLY40
A	PHE64-GLY84
A	ALA131-TYR151
A	LEU186-LEU203
B	ILE20-GLY40
B	PHE64-GLY84
B	ALA131-TYR151
B	LEU186-LEU203

site_id	SWS_FT_FI3
Number of Residues	110
Details	TOPO_DOM: Periplasmic => ECO:0000255

Chain	Residue	Details
A	LYS41-HIS63
A	SER152-ARG185
B	LYS41-HIS63
B	SER152-ARG185

site_id	SWS_FT_FI4
Number of Residues	44
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P21853

Chain	Residue	Details
S	CYS17
S	CYS249
S	CYS252
T	CYS17
T	CYS20
T	CYS115
T	CYS149
T	HIS187
T	CYS190
T	CYS215
T	CYS221
S	CYS20
T	CYS230
T	CYS249
T	CYS252
Q	CYS17
Q	CYS20
Q	CYS115
Q	CYS149
Q	HIS187
Q	CYS190
Q	CYS215
S	CYS115
Q	CYS221
Q	CYS230
Q	CYS249
Q	CYS252
R	CYS17
R	CYS20
R	CYS115
R	CYS149
R	HIS187
R	CYS190
S	CYS149
R	CYS215
R	CYS221
R	CYS230
R	CYS249
R	CYS252
S	HIS187
S	CYS190
S	CYS215
S	CYS221
S	CYS230

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