Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3M9S

Crystal structure of respiratory complex I from Thermus thermophilus

Functional Information from GO Data

Chain	GOid	namespace	contents
1	0005886	cellular_component	plasma membrane
1	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
1	0010181	molecular_function	FMN binding
1	0046872	molecular_function	metal ion binding
1	0048038	molecular_function	quinone binding
1	0051287	molecular_function	NAD binding
1	0051536	molecular_function	iron-sulfur cluster binding
1	0051539	molecular_function	4 iron, 4 sulfur cluster binding
1	1902600	biological_process	proton transmembrane transport
2	0003954	molecular_function	NADH dehydrogenase activity
2	0005886	cellular_component	plasma membrane
2	0016491	molecular_function	oxidoreductase activity
2	0046872	molecular_function	metal ion binding
2	0048038	molecular_function	quinone binding
2	0051536	molecular_function	iron-sulfur cluster binding
2	0051537	molecular_function	2 iron, 2 sulfur cluster binding
3	0005886	cellular_component	plasma membrane
3	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
3	0016020	cellular_component	membrane
3	0016491	molecular_function	oxidoreductase activity
3	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
3	0042773	biological_process	ATP synthesis coupled electron transport
3	0043546	molecular_function	molybdopterin cofactor binding
3	0046872	molecular_function	metal ion binding
3	0048038	molecular_function	quinone binding
3	0051536	molecular_function	iron-sulfur cluster binding
3	0051537	molecular_function	2 iron, 2 sulfur cluster binding
3	0051539	molecular_function	4 iron, 4 sulfur cluster binding
3	1902600	biological_process	proton transmembrane transport
4	0005886	cellular_component	plasma membrane
4	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
4	0048038	molecular_function	quinone binding
4	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
4	0051287	molecular_function	NAD binding
5	0005886	cellular_component	plasma membrane
5	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
5	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
5	0048038	molecular_function	quinone binding
5	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
5	1902600	biological_process	proton transmembrane transport
6	0005506	molecular_function	iron ion binding
6	0005886	cellular_component	plasma membrane
6	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
6	0009060	biological_process	aerobic respiration
6	0015990	biological_process	electron transport coupled proton transport
6	0045271	cellular_component	respiratory chain complex I
6	0046872	molecular_function	metal ion binding
6	0048038	molecular_function	quinone binding
6	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
6	0051536	molecular_function	iron-sulfur cluster binding
6	0051539	molecular_function	4 iron, 4 sulfur cluster binding
7	0005886	cellular_component	plasma membrane
7	0008199	molecular_function	ferric iron binding
7	0016226	biological_process	iron-sulfur cluster assembly
7	0048038	molecular_function	quinone binding
9	0003954	molecular_function	NADH dehydrogenase activity
9	0005506	molecular_function	iron ion binding
9	0005886	cellular_component	plasma membrane
9	0009060	biological_process	aerobic respiration
9	0016020	cellular_component	membrane
9	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
9	0046872	molecular_function	metal ion binding
9	0048038	molecular_function	quinone binding
9	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
9	0051536	molecular_function	iron-sulfur cluster binding
9	0051539	molecular_function	4 iron, 4 sulfur cluster binding
A	0005886	cellular_component	plasma membrane
A	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
A	0010181	molecular_function	FMN binding
A	0046872	molecular_function	metal ion binding
A	0048038	molecular_function	quinone binding
A	0051287	molecular_function	NAD 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	0003954	molecular_function	NADH dehydrogenase activity
B	0005886	cellular_component	plasma membrane
B	0016491	molecular_function	oxidoreductase activity
B	0046872	molecular_function	metal ion binding
B	0048038	molecular_function	quinone binding
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051537	molecular_function	2 iron, 2 sulfur cluster binding
C	0005886	cellular_component	plasma membrane
C	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
C	0042773	biological_process	ATP synthesis coupled electron transport
C	0043546	molecular_function	molybdopterin cofactor binding
C	0046872	molecular_function	metal ion binding
C	0048038	molecular_function	quinone binding
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051537	molecular_function	2 iron, 2 sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	1902600	biological_process	proton transmembrane transport
D	0005886	cellular_component	plasma membrane
D	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
D	0048038	molecular_function	quinone binding
D	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
D	0051287	molecular_function	NAD binding
E	0005886	cellular_component	plasma membrane
E	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
E	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
E	0048038	molecular_function	quinone binding
E	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
E	1902600	biological_process	proton transmembrane transport
F	0005506	molecular_function	iron ion binding
F	0005886	cellular_component	plasma membrane
F	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
F	0009060	biological_process	aerobic respiration
F	0015990	biological_process	electron transport coupled proton transport
F	0045271	cellular_component	respiratory chain complex I
F	0046872	molecular_function	metal ion binding
F	0048038	molecular_function	quinone binding
F	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
F	0051536	molecular_function	iron-sulfur cluster binding
F	0051539	molecular_function	4 iron, 4 sulfur cluster binding
G	0003954	molecular_function	NADH dehydrogenase activity
G	0005506	molecular_function	iron ion binding
G	0005886	cellular_component	plasma membrane
G	0009060	biological_process	aerobic respiration
G	0016020	cellular_component	membrane
G	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
G	0046872	molecular_function	metal ion binding
G	0048038	molecular_function	quinone binding
G	0050136	molecular_function	NADH dehydrogenase (quinone) (non-electrogenic) activity
G	0051536	molecular_function	iron-sulfur cluster binding
G	0051539	molecular_function	4 iron, 4 sulfur cluster binding
J	0005886	cellular_component	plasma membrane
J	0008199	molecular_function	ferric iron binding
J	0016226	biological_process	iron-sulfur cluster assembly
J	0048038	molecular_function	quinone binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 6 182

Chain	Residue
4	ARG84
6	PRO141
4	HIS169
6	CYS45
6	CYS46
6	GLY82
6	ARG83
6	ALA110
6	CYS111
6	CYS140

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 9 183

Chain	Residue
9	HIS41
9	CYS63
9	ILE68
9	CYS98
9	ILE99
9	PHE100
9	CYS101
9	GLY102
9	CYS104

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 9 184

Chain	Residue
9	CYS53
9	ILE54
9	CYS56
9	SER57
9	CYS59
9	CYS108
9	PRO109
9	THR110
9	ALA112
9	ILE113

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 3 784

Chain	Residue
3	HIS115
3	ASP118
3	CYS119
3	CYS122
3	CYS128
3	LEU130
3	GLN131
3	VAL232
3	GLY233

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 3 785

Chain	Residue
3	CYS181
3	ILE182
3	CYS184
3	ARG186
3	CYS187
3	CYS230
3	PRO231
3	ALA234

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 3 786

Chain	Residue
3	CYS256
3	LEU258
3	CYS259
3	VAL261
3	GLY262
3	CYS263
3	CYS291
3	GLY294
3	PRO407
3	ILE408

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FES 3 787

Chain	Residue
3	LEU32
3	CYS34
3	SER35
3	GLY43
3	ALA44
3	CYS45
3	ARG46
3	CYS48
3	CYS83

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 1 439

Chain	Residue
1	PRO199
1	SER352
1	CYS353
1	GLY354
1	LYS355
1	CYS356
1	CYS359
1	CYS400
1	LEU402
1	ALA403

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FES 2 182

Chain	Residue
2	CYS83
2	THR85
2	SER87
2	CYS88
2	CYS124
2	LEU125
2	GLY126
2	SER127
2	CYS128

site_id	BC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE FMN 1 440

Chain	Residue
1	GLY64
1	GLY66
1	LYS75
1	ASN92
1	ASP94
1	SER96
1	GLY183
1	GLU184
1	GLU185
1	ILE218
1	ASN219
1	ASN220
1	THR223
1	PRO401
1	LEU402

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 F 182

Chain	Residue
D	ARG84
D	HIS169
F	CYS45
F	CYS46
F	GLY82
F	ARG83
F	ALA110
F	CYS111
F	CYS140
F	PRO141

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 G 183

Chain	Residue
G	HIS41
G	CYS63
G	ILE68
G	CYS98
G	ILE99
G	PHE100
G	CYS101
G	GLY102
G	CYS104

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 G 184

Chain	Residue
G	CYS53
G	ILE54
G	CYS56
G	SER57
G	CYS59
G	CYS108
G	PRO109
G	THR110
G	ALA112
G	ILE113

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 C 784

Chain	Residue
C	HIS115
C	ASP118
C	CYS119
C	CYS122
C	CYS128
C	LEU130
C	GLN131
C	VAL232
C	GLY233

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 C 785

Chain	Residue
C	CYS181
C	ILE182
C	CYS184
C	ARG186
C	CYS187
C	CYS230
C	PRO231
C	ALA234

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 C 786

Chain	Residue
C	CYS256
C	LEU258
C	CYS259
C	VAL261
C	GLY262
C	CYS263
C	CYS291
C	GLY294
C	PRO407
C	ILE408

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FES C 787

Chain	Residue
C	LEU32
C	CYS34
C	SER35
C	GLY43
C	ALA44
C	CYS45
C	ARG46
C	CYS48
C	CYS83

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 A 439

Chain	Residue
A	PRO199
A	SER352
A	CYS353
A	GLY354
A	LYS355
A	CYS356
A	CYS359
A	CYS400
A	LEU402
A	ALA403

site_id	CC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FES B 182

Chain	Residue
B	CYS83
B	THR85
B	SER87
B	CYS88
B	CYS124
B	LEU125
B	GLY126
B	SER127
B	CYS128

site_id	CC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE FMN A 440

Chain	Residue
A	GLY64
A	GLY66
A	LYS75
A	ASN92
A	ASP94
A	SER96
A	GLY183
A	GLU184
A	GLU185
A	ILE218
A	ASN219
A	ASN220
A	THR223
A	PRO401
A	LEU402

Functional Information from PROSITE/UniProt

site_id	PS00198
Number of Residues	12
Details	4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CiGCSlCAaACP

Chain	Residue	Details
9	CYS53-PRO64
9	CYS98-PRO109

site_id	PS00535
Number of Residues	12
Details	COMPLEX1_49K Respiratory chain NADH dehydrogenase 49 Kd subunit signature. LHTGfEKTmEhR

Chain	Residue	Details
4	LEU62-ARG73

site_id	PS00542
Number of Residues	22
Details	COMPLEX1_30K Respiratory chain NADH dehydrogenase 30 Kd subunit signature. EREvyDLFgivfegHpdlRkIL

Chain	Residue	Details
5	GLU115-LEU136

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

Chain	Residue	Details
3	PRO31-CYS48

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

Chain	Residue	Details
3	CYS119-GLN131

site_id	PS00643
Number of Residues	11
Details	COMPLEX1_75K_3 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. RCIhCkRCVrY

Chain	Residue	Details
3	ARG180-TYR190

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

Chain	Residue	Details
1	GLY176-SER191

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

Chain	Residue	Details
1	GLU351-GLY362

site_id	PS01099
Number of Residues	19
Details	COMPLEX1_24K Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. DglFSvqkveCLGsChtAP

Chain	Residue	Details
2	ASP114-PRO132

site_id	PS01150
Number of Residues	17
Details	COMPLEX1_20K Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. NvDSVVPVDVYvPgCPP

Chain	Residue	Details
6	ASN126-PRO142

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	94
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16469879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	78
Details	Domain: {"description":"4Fe-4S His(Cys)3-ligated-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01184","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	112
Details	Domain: {"description":"4Fe-4S Mo/W bis-MGD-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01004","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01184","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16469879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01184","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	60
Details	Domain: {"description":"4Fe-4S ferredoxin-type 1"}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	58
Details	Domain: {"description":"4Fe-4S ferredoxin-type 2"}

Chain

Residue

Details

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