Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5A4I

The mechanism of Hydrogen activation by NiFE-hydrogenases

Functional Information from GO Data

Chain	GOid	namespace	contents
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
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	13
Details	BINDING SITE FOR RESIDUE FCO L 601

Chain	Residue
L	CSO79
L	THR532
L	CYS579
L	NI602
L	HOH2065
L	VAL82
L	HIS83
L	ALA507
L	PRO508
L	ARG509
L	LEU512
L	VAL530
L	PRO531

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI L 602

Chain	Residue
L	CYS76
L	CSO79
L	CYS576
L	CYS579
L	FCO601
L	HOH2065

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG L 603

Chain	Residue
L	GLU57
L	CYS528
L	HIS582
L	HOH2043
L	HOH2044
L	HOH2252

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 M 604

Chain	Residue
M	ARG394
S	ARG125

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO M 601

Chain	Residue
M	CSO79
M	VAL82
M	HIS83
M	ALA507
M	PRO508
M	ARG509
M	LEU512
M	VAL530
M	PRO531
M	THR532
M	CYS579
M	NI602
M	HOH2069

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI M 602

Chain	Residue
M	CYS76
M	CSO79
M	CYS576
M	CYS579
M	FCO601
M	HOH2069

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG M 603

Chain	Residue
M	GLU57
M	CYS528
M	HIS582
M	HOH2047
M	HOH2048
M	HOH2257

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 M 604

Chain	Residue
M	ARG394
S	ARG125

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SF4 S 401

Chain	Residue
S	HIS187
S	CYS190
S	ARG193
S	CYS215
S	LEU216
S	CYS221

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S S 402

Chain	Residue
L	LYS226
S	THR226
S	ASN228
S	CYS230
S	TRP235
S	PRO242
S	CYS249
S	LEU250
S	CYS252

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF3 S 403

Chain	Residue
S	GLU16
S	CYS17
S	THR18
S	CYS19
S	THR114
S	CYS115
S	CYS120
S	GLY148
S	CYS149
S	HOH2003

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT S 404

Chain	Residue
S	ILE7
S	TRP11
S	ILE72
S	MET163
S	ARG168

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL S 405

Chain	Residue
S	TRP118
S	CYS120
S	GLY256
S	HOH2044

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL S 406

Chain	Residue
S	ILE12
S	HIS13
S	ASP46
S	LYS98
S	HOH2002

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 S 407

Chain	Residue
L	GLY480
L	ASN481
L	LEU482
L	ALA483
S	ARG211

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SF4 T 401

Chain	Residue
T	CYS190
T	ARG193
T	CYS215
T	LEU216
T	CYS221
T	HIS187

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S T 402

Chain	Residue
M	LYS226
T	THR226
T	ASN228
T	CYS230
T	TRP235
T	PRO242
T	CYS249
T	LEU250
T	CYS252

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF3 T 403

Chain	Residue
T	GLU16
T	CYS17
T	THR18
T	CYS19
T	THR114
T	CYS115
T	CYS120
T	GLY148
T	CYS149

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LMT T 404

Chain	Residue
T	ILE7
T	TRP11
T	MET163
T	VAL164

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL T 405

Chain	Residue
T	TRP118
T	CYS120
T	GLY256
T	HOH2034

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL T 406

Chain	Residue
T	ILE12
T	HIS13
T	ASP46
T	LYS98

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-CSO79

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	558
Details	TOPO_DOM: Periplasmic => ECO:0000255

Chain	Residue	Details
S	LEU1-ASP280
T	LEU1-ASP280
L	CYS576
L	CYS579
M	CYS76
M	CSO79
M	CYS576
M	CYS579

site_id	SWS_FT_FI2
Number of Residues	44
Details	TRANSMEM: Helical => ECO:0000255

Chain	Residue	Details
S	THR281-VAL303
T	THR281-VAL303

site_id	SWS_FT_FI3
Number of Residues	46
Details	TOPO_DOM: Cytoplasmic => ECO:0000255

Chain	Residue	Details
S	ASP304-ALA327
T	ASP304-ALA327

site_id	SWS_FT_FI4
Number of Residues	22
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
S	CYS115
S	CYS149
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)