Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3MYR

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0051536	molecular_function	iron-sulfur cluster binding
B	0005886	cellular_component	plasma membrane
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0016151	molecular_function	nickel cation binding
B	0016491	molecular_function	oxidoreductase activity
B	0033748	molecular_function	hydrogenase (acceptor) activity
B	0046872	molecular_function	metal ion binding
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0051536	molecular_function	iron-sulfur cluster binding
D	0005886	cellular_component	plasma membrane
D	0008901	molecular_function	ferredoxin hydrogenase activity
D	0016151	molecular_function	nickel cation binding
D	0016491	molecular_function	oxidoreductase activity
D	0033748	molecular_function	hydrogenase (acceptor) activity
D	0046872	molecular_function	metal ion binding
E	0008901	molecular_function	ferredoxin hydrogenase activity
E	0009375	cellular_component	ferredoxin hydrogenase complex
E	0051536	molecular_function	iron-sulfur cluster binding
F	0005886	cellular_component	plasma membrane
F	0008901	molecular_function	ferredoxin hydrogenase activity
F	0016151	molecular_function	nickel cation binding
F	0016491	molecular_function	oxidoreductase activity
F	0033748	molecular_function	hydrogenase (acceptor) activity
F	0046872	molecular_function	metal ion binding
G	0008901	molecular_function	ferredoxin hydrogenase activity
G	0009375	cellular_component	ferredoxin hydrogenase complex
G	0051536	molecular_function	iron-sulfur cluster binding
H	0005886	cellular_component	plasma membrane
H	0008901	molecular_function	ferredoxin hydrogenase activity
H	0016151	molecular_function	nickel cation binding
H	0016491	molecular_function	oxidoreductase activity
H	0033748	molecular_function	hydrogenase (acceptor) activity
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE SF4 A 2001

Chain	Residue
A	GLU15
A	GLY148
A	CYS149
A	PRO150
B	ARG1059
A	CYS16
A	THR17
A	GLY18
A	CYS19
A	ASP75
A	GLY113
A	THR114
A	CYS115

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 A 2002

Chain	Residue
A	HIS187
A	CYS190
A	ARG192
A	ARG193
A	CYS215
A	LEU216
A	CYS221

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE F3S A 2003

Chain	Residue
A	THR226
A	ASN228
A	CYS230
A	TRP235
A	CYS249
A	LEU250
A	CYS252

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE IMD A 3002

Chain	Residue
A	VAL143
A	ASN145
A	GLY176
A	HOH3657
G	ARG139
G	HOH5826

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL A 2004

Chain	Residue
A	PRO153
A	MET154
A	ASN236
A	ASP237
A	HOH3328

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NFV B 2005

Chain	Residue
B	CYS1061
B	CYS1064
B	VAL1067
B	HIS1068
B	ALA1485
B	PRO1486
B	ARG1487
B	LEU1490
B	VAL1508
B	PRO1509
B	SER1510
B	CYS1555
B	CYS1558

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 2006

Chain	Residue
B	GLU1042
B	ALA1506
B	HIS1561
B	HOH2007
B	HOH2008
B	HOH2009

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL C 2004

Chain	Residue
C	PRO153
C	MET154
C	ASN236
C	ASP237
C	HOH3354

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE SF4 C 2001

Chain	Residue
C	GLU15
C	CYS16
C	THR17
C	GLY18
C	CYS19
C	ASP75
C	GLY113
C	THR114
C	CYS115
C	GLY148
C	CYS149
C	PRO150
C	HOH5613

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 C 2002

Chain	Residue
C	ILE186
C	HIS187
C	CYS190
C	ARG192
C	ARG193
C	CYS215
C	LEU216
C	CYS221

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S C 2003

Chain	Residue
C	THR226
C	ASN228
C	CYS230
C	TRP235
C	PRO242
C	CYS249
C	LEU250
C	CYS252
D	LYS1211

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NFV D 2005

Chain	Residue
D	LEU1490
D	VAL1508
D	PRO1509
D	SER1510
D	CYS1555
D	CYS1558
D	CYS1061
D	CYS1064
D	VAL1067
D	HIS1068
D	ALA1485
D	PRO1486
D	ARG1487

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 2006

Chain	Residue
D	GLU1042
D	ALA1506
D	HIS1561
D	HOH2007
D	HOH2008
D	HOH2009

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE SF4 E 2001

Chain	Residue
E	GLU15
E	CYS16
E	THR17
E	GLY18
E	CYS19
E	ASP75
E	GLY113
E	THR114
E	CYS115
E	GLY148
E	CYS149
E	PRO150
E	HOH5628
F	ARG1059
F	HIS1214

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 E 2002

Chain	Residue
E	ILE186
E	HIS187
E	CYS190
E	ARG192
E	ARG193
E	CYS215
E	LEU216
E	CYS221

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S E 2003

Chain	Residue
E	THR226
E	ASN228
E	CYS230
E	TRP235
E	PRO242
E	CYS249
E	LEU250
E	CYS252
F	LYS1211

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL E 2004

Chain	Residue
E	PRO153
E	MET154
E	ASN236
E	ASP237

site_id	BC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE NFV F 2005

Chain	Residue
F	CYS1061
F	CYS1064
F	VAL1067
F	HIS1068
F	ALA1485
F	PRO1486
F	ARG1487
F	VAL1508
F	PRO1509
F	SER1510
F	CYS1555
F	CYS1558

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 2006

Chain	Residue
F	GLU1042
F	ALA1506
F	HIS1561
F	HOH2007
F	HOH2008
F	HOH2009

site_id	CC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE SF4 G 2001

Chain	Residue
G	GLU15
G	CYS16
G	THR17
G	GLY18
G	CYS19
G	ASP75
G	GLY113
G	THR114
G	CYS115
G	GLY148
G	CYS149
G	PRO150
H	HIS1214

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 G 2002

Chain	Residue
G	HIS187
G	CYS190
G	ARG192
G	ARG193
G	CYS215
G	LEU216
G	CYS221

site_id	CC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S G 2003

Chain	Residue
G	ASN228
G	CYS230
G	TRP235
G	TRP241
G	CYS249
G	LEU250
G	CYS252
H	LYS1211

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL G 2004

Chain	Residue
G	PRO153
G	MET154
G	ASN236
G	ASP237
G	HOH3053

site_id	CC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE IMD G 3001

Chain	Residue
A	ARG139
A	HOH4142
G	MET135
G	VAL143
G	ASN145
G	GLY176
G	HOH4119

site_id	CC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NFV H 2005

Chain	Residue
H	CYS1061
H	CYS1064
H	VAL1067
H	HIS1068
H	ALA1485
H	PRO1486
H	ARG1487
H	LEU1490
H	VAL1508
H	PRO1509
H	SER1510
H	CYS1555
H	CYS1558

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 2006

Chain	Residue
H	GLU1042
H	ALA1506
H	HIS1561
H	HOH2007
H	HOH2008
H	HOH2009

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	ARG1039-CYS1064

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

Chain	Residue	Details
B	PHE1552-HIS1561

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