Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5XF9

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
A	0010181	molecular_function	FMN binding
A	0046872	molecular_function	metal ion binding
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
A	1902600	biological_process	proton transmembrane transport
B	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0042773	biological_process	ATP synthesis coupled electron transport
B	0046872	molecular_function	metal ion binding
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051537	molecular_function	2 iron, 2 sulfur cluster binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	1902600	biological_process	proton transmembrane transport
C	0016491	molecular_function	oxidoreductase activity
C	0046872	molecular_function	metal ion binding
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
D	0008901	molecular_function	ferredoxin hydrogenase activity
D	0016151	molecular_function	nickel cation binding
D	0016491	molecular_function	oxidoreductase activity
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
E	0010181	molecular_function	FMN binding
E	0046872	molecular_function	metal ion binding
E	0051536	molecular_function	iron-sulfur cluster binding
E	0051539	molecular_function	4 iron, 4 sulfur cluster binding
E	1902600	biological_process	proton transmembrane transport
F	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
F	0016020	cellular_component	membrane
F	0016491	molecular_function	oxidoreductase activity
F	0042773	biological_process	ATP synthesis coupled electron transport
F	0046872	molecular_function	metal ion binding
F	0051536	molecular_function	iron-sulfur cluster binding
F	0051537	molecular_function	2 iron, 2 sulfur cluster binding
F	0051539	molecular_function	4 iron, 4 sulfur cluster binding
F	1902600	biological_process	proton transmembrane transport
G	0016491	molecular_function	oxidoreductase activity
G	0046872	molecular_function	metal ion binding
G	0051536	molecular_function	iron-sulfur cluster binding
G	0051538	molecular_function	3 iron, 4 sulfur cluster binding
G	0051539	molecular_function	4 iron, 4 sulfur cluster binding
H	0008901	molecular_function	ferredoxin hydrogenase activity
H	0016151	molecular_function	nickel cation binding
H	0016491	molecular_function	oxidoreductase activity
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	binding site for residue FMN A 601

Chain	Residue
A	GLY202
A	GLY317
A	GLU318
A	GLU319
A	VAL352
A	ASN353
A	ASN354
A	THR357
A	PHE527
A	GLU585
A	HOH703
A	ARG203
A	HOH712
A	HOH721
A	HOH754
A	HOH812
A	GLY204
A	LYS213
A	ASN230
A	ASP232
A	GLU233
A	GLY234
A	TYR314

site_id	AC2
Number of Residues	9
Details	binding site for residue SF4 A 602

Chain	Residue
A	SER478
A	CYS479
A	GLY480
A	PHE481
A	CYS482
A	CYS485
A	ASN524
A	CYS525
A	PHE527

site_id	AC3
Number of Residues	8
Details	binding site for residue SF4 B 301

Chain	Residue
B	PHE98
B	HIS103
B	PHE104
B	CYS105
B	CYS108
B	SER111
B	CYS114
B	GLY209

site_id	AC4
Number of Residues	8
Details	binding site for residue SF4 B 302

Chain	Residue
B	CYS153
B	ILE154
B	CYS156
B	GLY157
B	CYS159
B	CYS206
B	VAL208
B	ALA210

site_id	AC5
Number of Residues	7
Details	binding site for residue FES B 303

Chain	Residue
B	HIS41
B	CYS43
B	GLY52
B	CYS54
B	ARG55
B	CYS57
B	CYS69

site_id	AC6
Number of Residues	9
Details	binding site for residue SF4 C 201

Chain	Residue
C	CYS24
C	CYS27
C	GLU67
C	ALA94
C	CYS95
C	CYS159
C	PRO160
D	ARG78
D	HIS183

site_id	AC7
Number of Residues	12
Details	binding site for residue FCO D 501

Chain	Residue
D	CYS83
D	SER86
D	ALA394
D	PRO395
D	ARG396
D	LEU399
D	VAL418
D	SER419
D	THR420
D	CYS462
D	CYS465
D	3NI502

site_id	AC8
Number of Residues	6
Details	binding site for residue 3NI D 502

Chain	Residue
D	GLU32
D	CYS80
D	CYS83
D	CYS462
D	CYS465
D	FCO501

site_id	AC9
Number of Residues	6
Details	binding site for residue MG D 503

Chain	Residue
D	GLU61
D	LEU416
D	HIS468
D	HOH609
D	HOH634
D	HOH647

site_id	AD1
Number of Residues	23
Details	binding site for residue FMN E 601

Chain	Residue
E	VAL352
E	ASN353
E	ASN354
E	THR357
E	GLY526
E	PHE527
E	GLU585
E	HOH701
E	HOH708
E	HOH710
E	HOH736
E	HOH737
E	GLY202
E	ARG203
E	GLY204
E	LYS213
E	ASN230
E	ASP232
E	GLY234
E	TYR314
E	GLY317
E	GLU318
E	GLU319

site_id	AD2
Number of Residues	11
Details	binding site for residue SF4 E 602

Chain	Residue
E	SER478
E	CYS479
E	GLY480
E	PHE481
E	CYS482
E	CYS485
E	SER523
E	ASN524
E	CYS525
E	PHE527
E	GLY528

site_id	AD3
Number of Residues	8
Details	binding site for residue SF4 F 301

Chain	Residue
F	HIS103
F	PHE104
F	CYS105
F	CYS108
F	SER111
F	CYS114
F	GLN117
F	GLY209

site_id	AD4
Number of Residues	7
Details	binding site for residue SF4 F 302

Chain	Residue
F	CYS153
F	ILE154
F	CYS156
F	GLY157
F	CYS159
F	CYS206
F	VAL208

site_id	AD5
Number of Residues	7
Details	binding site for residue FES F 303

Chain	Residue
F	HIS41
F	CYS43
F	GLY52
F	CYS54
F	ARG55
F	CYS57
F	CYS69

site_id	AD6
Number of Residues	12
Details	binding site for residue SF4 G 201

Chain	Residue
G	GLY23
G	CYS24
G	CYS27
G	GLU67
G	GLY93
G	ALA94
G	CYS95
G	GLY158
G	CYS159
G	PRO160
H	ARG78
H	HIS183

site_id	AD7
Number of Residues	13
Details	binding site for residue FCO H 501

Chain	Residue
H	CYS83
H	SER86
H	HIS87
H	ALA394
H	PRO395
H	ARG396
H	LEU399
H	VAL418
H	SER419
H	THR420
H	CYS462
H	CYS465
H	3NI502

site_id	AD8
Number of Residues	6
Details	binding site for residue 3NI H 502

Chain	Residue
H	GLU32
H	CYS80
H	CYS83
H	CYS462
H	CYS465
H	FCO501

site_id	AD9
Number of Residues	6
Details	binding site for residue MG H 503

Chain	Residue
H	GLU61
H	LEU416
H	HIS468
H	HOH641
H	HOH667
H	HOH669

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
D	ARG58-CYS83

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

Chain	Residue	Details
D	PHE459-HIS468

site_id	PS00641
Number of Residues	18
Details	COMPLEX1_75K_1 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. PhlCWhpemgnhGsCRlC

Chain	Residue	Details
B	PRO40-CYS57

site_id	PS00642
Number of Residues	13
Details	COMPLEX1_75K_2 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. CPgCEkSGdClLQ

Chain	Residue	Details
B	CYS105-GLN117

site_id	PS00644
Number of Residues	16
Details	COMPLEX1_51K_1 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. GAGAYVCGEESALIES

Chain	Residue	Details
A	GLY310-SER325

site_id	PS00645
Number of Residues	12
Details	COMPLEX1_51K_2 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ESCGfCtPCRvG

Chain	Residue	Details
A	GLU477-GLY488

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