Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1YQ9

Structure of the unready oxidized form of [NiFe] 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
H	0008901	molecular_function	ferredoxin hydrogenase activity
H	0016151	molecular_function	nickel cation binding
H	0016491	molecular_function	oxidoreductase activity
H	0042597	cellular_component	periplasmic space
H	0046872	molecular_function	metal ion binding
H	0047806	molecular_function	cytochrome-c3 hydrogenase activity
I	0008901	molecular_function	ferredoxin hydrogenase activity
I	0016151	molecular_function	nickel cation binding
I	0016491	molecular_function	oxidoreductase activity
I	0042597	cellular_component	periplasmic space
I	0046872	molecular_function	metal ion binding
I	0047806	molecular_function	cytochrome-c3 hydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI H 538

Chain	Residue
H	CYS65
H	CYS68
H	CYS530
H	CYS533
H	FCO537
H	PER539

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI I 538

Chain	Residue
I	CYS533
I	FCO537
I	PER539
I	CYS65
I	CYS68
I	CYS530

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 540

Chain	Residue
H	GLU46
H	LEU482
H	HIS536
H	HOH5011
H	HOH5012
H	HOH5013

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG I 540

Chain	Residue
I	GLU46
I	LEU482
I	HIS536
I	HOH5024
I	HOH5025
I	HOH5026

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 A 265

Chain	Residue
A	HIS185
A	CYS188
A	ARG190
A	LEU191
A	CYS213
A	LEU214
A	CYS219

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE F3S A 266

Chain	Residue
A	THR224
A	ASN226
A	CYS228
A	PHE233
A	TRP238
A	CYS246
A	ILE247
A	CYS249
H	LYS216
H	GLN221

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 A 267

Chain	Residue
A	GLU16
A	CYS17
A	CYS20
A	THR111
A	CYS112
A	GLY147
A	CYS148
A	PRO149
H	ARG63

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE H2S A 1268

Chain	Residue
A	GLY117
A	ASN253
A	HOH1551

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE FCO H 537

Chain	Residue
H	CYS68
H	VAL71
H	HIS72
H	ALA461
H	PRO462
H	ARG463
H	LEU466
H	PRO485
H	SER486
H	CYS533
H	NI538
H	PER539

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PER H 539

Chain	Residue
H	CYS65
H	CYS68
H	ARG463
H	CYS530
H	CYS533
H	FCO537
H	NI538

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE H2S H 1541

Chain	Residue
H	ARG55
H	VAL225
H	HOH5059

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 B 265

Chain	Residue
B	HIS185
B	CYS188
B	ARG190
B	LEU191
B	CYS213
B	LEU214
B	CYS219

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S B 266

Chain	Residue
B	ASN226
B	CYS228
B	PHE233
B	TRP238
B	CYS246
B	ILE247
B	CYS249
I	LYS216
I	GLN221

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 B 267

Chain	Residue
I	ARG63
B	CYS17
B	CYS20
B	GLY110
B	THR111
B	CYS112
B	GLY147
B	CYS148
B	PRO149

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE H2S B 2268

Chain	Residue
B	TYR115
B	GLY117
B	ASN253
B	HOH291

site_id	BC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FCO I 537

Chain	Residue
I	CYS68
I	HIS72
I	ALA461
I	PRO462
I	ARG463
I	VAL484
I	PRO485
I	SER486
I	CYS533
I	NI538
I	PER539

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PER I 539

Chain	Residue
I	CYS68
I	ARG463
I	CYS530
I	CYS533
I	FCO537
I	NI538

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE H2S I 2541

Chain	Residue
I	ARG55
I	VAL224
I	VAL225
I	HOH5061
I	HOH5071

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 1271

Chain	Residue
A	HIS54
A	GLY88
A	ARG90
A	GOL1272
A	HOH1562
B	PHE194

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 1272

Chain	Residue
A	GLU57
A	LEU60
A	HIS61
A	ILE64
A	ARG90
A	GLU98
A	GOL1271
B	PHE194
B	TYR215

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 1273

Chain	Residue
A	LYS102
A	HOH1639
A	HOH1642
B	LEU257
B	ALA264
B	HOH313
B	HOH328

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 1542

Chain	Residue
A	ALA208
A	LYS209
A	GLY211
A	HOH1549
A	HOH1655
H	ASP232

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL H 1543

Chain	Residue
A	GLY89
B	GLY197
B	HOH326
B	HOH355
H	GLU347
H	PHE348
H	HOH5136

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL H 1544

Chain	Residue
H	VAL84
H	ASN128
H	ASP446
H	TRP447
H	GLN448
H	HOH5021

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 2542

Chain	Residue
B	ALA208
B	LYS209
B	GLY211
B	HOH375
I	ASP232

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
H	ARG43-CYS68

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

Chain	Residue	Details
H	TYR527-HIS536

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:7854413

Chain	Residue	Details
H	GLY66
A	CYS246
A	CYS249
B	CYS17
B	CYS20
B	CYS112
B	CYS148
B	HIS185
B	CYS188
B	CYS213
B	CYS219
H	ILE531
B	CYS228
B	CYS246
B	CYS249
I	GLY66
I	ILE531
A	HIS185
A	CYS188
A	CYS213
A	CYS219
A	CYS228

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING:

Chain	Residue	Details
H	THR69
H	GLY534
I	THR69
I	GLY534

Catalytic Information from CSA

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

Chain	Residue	Details
A	THR18
H	CYS530
H	GLU18

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

Chain	Residue	Details
I	CYS530
I	GLU18
B	THR18

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

Chain	Residue	Details
H	CYS530

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

Chain	Residue	Details
I	CYS530

site_id	MCSA1
Number of Residues	8
Details	M-CSA 126

Chain	Residue	Details
H	GLY19	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
H	GLY66	activator, metal ligand
H	THR69	activator, electrostatic stabiliser, metal ligand
H	ALA73	electrostatic stabiliser, hydrogen bond donor
H	GLY464	electrostatic stabiliser, hydrogen bond donor
H	THR487	electrostatic stabiliser, hydrogen bond donor
H	ILE531	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
H	GLY534	activator, electrostatic stabiliser, metal ligand

site_id	MCSA2
Number of Residues	8
Details	M-CSA 126

Chain	Residue	Details
I	GLY19	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
I	GLY66	activator, metal ligand
I	THR69	activator, electrostatic stabiliser, metal ligand
I	ALA73	electrostatic stabiliser, hydrogen bond donor
I	GLY464	electrostatic stabiliser, hydrogen bond donor
I	THR487	electrostatic stabiliser, hydrogen bond donor
I	ILE531	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
I	GLY534	activator, electrostatic stabiliser, metal ligand

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