Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5XTB

Cryo-EM structure of human respiratory complex I matrix arm

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005739	cellular_component	mitochondrion
A	0005743	cellular_component	mitochondrial inner membrane
A	0006120	biological_process	mitochondrial electron transport, NADH to ubiquinone
A	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
A	0009060	biological_process	aerobic respiration
A	0010181	molecular_function	FMN binding
A	0016491	molecular_function	oxidoreductase activity
A	0042775	biological_process	mitochondrial ATP synthesis coupled electron transport
A	0042776	biological_process	proton motive force-driven mitochondrial ATP synthesis
A	0045271	cellular_component	respiratory chain complex I
A	0046872	molecular_function	metal ion 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	0016020	cellular_component	membrane
B	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
C	0048038	molecular_function	quinone binding
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
E	0045271	cellular_component	respiratory chain complex I
G	0006633	biological_process	fatty acid biosynthetic process
H	0005515	molecular_function	protein binding
H	0005739	cellular_component	mitochondrion
H	0005743	cellular_component	mitochondrial inner membrane
H	0006120	biological_process	mitochondrial electron transport, NADH to ubiquinone
H	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
H	0009060	biological_process	aerobic respiration
H	0022904	biological_process	respiratory electron transport chain
H	0032991	cellular_component	protein-containing complex
H	0042776	biological_process	proton motive force-driven mitochondrial ATP synthesis
H	0045271	cellular_component	respiratory chain complex I
H	1902600	biological_process	proton transmembrane transport
I	0005515	molecular_function	protein binding
I	0005739	cellular_component	mitochondrion
I	0005743	cellular_component	mitochondrial inner membrane
I	0006120	biological_process	mitochondrial electron transport, NADH to ubiquinone
I	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
I	0009060	biological_process	aerobic respiration
I	0042773	biological_process	ATP synthesis coupled electron transport
I	0042776	biological_process	proton motive force-driven mitochondrial ATP synthesis
I	0045271	cellular_component	respiratory chain complex I
I	1902600	biological_process	proton transmembrane transport
K	0005739	cellular_component	mitochondrion
K	0045271	cellular_component	respiratory chain complex I
L	0022900	biological_process	electron transport chain
M	0005515	molecular_function	protein binding
M	0005739	cellular_component	mitochondrion
M	0005743	cellular_component	mitochondrial inner membrane
M	0005758	cellular_component	mitochondrial intermembrane space
M	0005759	cellular_component	mitochondrial matrix
M	0006120	biological_process	mitochondrial electron transport, NADH to ubiquinone
M	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
M	0009055	molecular_function	electron transfer activity
M	0009060	biological_process	aerobic respiration
M	0016020	cellular_component	membrane
M	0016491	molecular_function	oxidoreductase activity
M	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
M	0032981	biological_process	mitochondrial respiratory chain complex I assembly
M	0042773	biological_process	ATP synthesis coupled electron transport
M	0042776	biological_process	proton motive force-driven mitochondrial ATP synthesis
M	0045271	cellular_component	respiratory chain complex I
M	0045333	biological_process	cellular respiration
M	0046872	molecular_function	metal ion binding
M	0051536	molecular_function	iron-sulfur cluster binding
M	0051537	molecular_function	2 iron, 2 sulfur cluster binding
M	0051539	molecular_function	4 iron, 4 sulfur cluster binding
M	1902600	biological_process	proton transmembrane transport
N	0005515	molecular_function	protein binding
N	0005739	cellular_component	mitochondrion
N	0005743	cellular_component	mitochondrial inner membrane
N	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
N	0009060	biological_process	aerobic respiration
N	0016020	cellular_component	membrane
N	0042775	biological_process	mitochondrial ATP synthesis coupled electron transport
N	0042776	biological_process	proton motive force-driven mitochondrial ATP synthesis
N	0045271	cellular_component	respiratory chain complex I
N	1902600	biological_process	proton transmembrane transport
O	0016491	molecular_function	oxidoreductase activity
P	0008137	molecular_function	NADH dehydrogenase (ubiquinone) activity
P	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
Q	0016651	molecular_function	oxidoreductase activity, acting on NAD(P)H
Q	0048038	molecular_function	quinone binding
Q	0051287	molecular_function	NAD binding
T	0006120	biological_process	mitochondrial electron transport, NADH to ubiquinone

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue SF4 A 501

Chain	Residue
A	ILE205
A	CYS425
A	PRO223
A	SER378
A	CYS379
A	GLN381
A	CYS382
A	CYS385
A	THR423
A	ILE424

site_id	AC2
Number of Residues	11
Details	binding site for residue FMN A 502

Chain	Residue
A	GLY87
A	ARG88
A	GLY89
A	ASN116
A	GLU119
A	GLY207
A	GLU208
A	GLU209
A	ALA243
A	ASN244
A	ALA426

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

Chain	Residue
B	CYS111
B	ALA113
B	CYS114
B	LYS115
B	CYS117
B	CYS160
B	ALA164
B	ILE165

site_id	AC4
Number of Residues	11
Details	binding site for residue SF4 B 302

Chain	Residue
B	HIS99
B	CYS121
B	PRO122
B	CYS150
B	ILE151
B	TYR152
B	CYS153
B	GLY154
B	PHE155
B	CYS156
B	GLU167

site_id	AC5
Number of Residues	9
Details	binding site for residue SF4 C 301

Chain	Residue
C	ALA87
C	CYS88
C	CYS89
C	GLY151
C	SER152
C	CYS153
C	CYS183
C	PRO184
Q	HIS223

site_id	AC6
Number of Residues	9
Details	binding site for residue 8Q1 E 201

Chain	Residue
E	MET25
E	TRP39
E	MET66
E	PHE67
E	ASN70
E	VAL79
E	LEU82
E	VAL83
G	SER112

site_id	AC7
Number of Residues	18
Details	binding site for residue NDP J 401

Chain	Residue
J	GLY60
J	THR62
J	GLY63
J	PHE64
J	LEU65
J	ALA110
J	LEU129
J	ILE130
J	GLY131
J	ARG132
J	PHE145
J	SER168
J	HIS169
J	TYR180
J	LYS184
J	PRO203
J	ILE206
J	ARG212

site_id	AC8
Number of Residues	9
Details	binding site for residue SF4 M 801

Chain	Residue
M	HIS124
M	ASP127
M	CYS128
M	CYS131
M	GLY134
M	CYS137
M	GLN140
M	VAL228
M	GLY229

site_id	AC9
Number of Residues	9
Details	binding site for residue SF4 M 802

Chain	Residue
M	CYS176
M	ILE177
M	CYS179
M	CYS182
M	CYS226
M	PRO227
M	VAL228
M	ALA230
M	LEU231

site_id	AD1
Number of Residues	9
Details	binding site for residue FES M 803

Chain	Residue
M	CYS75
M	MET77
M	CYS78
M	CYS92
M	ARG62
M	CYS64
M	TYR65
M	ALA72
M	ASN74

site_id	AD2
Number of Residues	9
Details	binding site for residue FES O 301

Chain	Residue
O	CYS135
O	THR137
O	PRO139
O	CYS140
O	CYS176
O	LEU177
O	GLY178
O	ALA179
O	CYS180

Functional Information from PROSITE/UniProt

site_id	PS00012
Number of Residues	16
Details	PHOSPHOPANTETHEINE Phosphopantetheine attachment site. DLGLDSLDQVEIIMAM

Chain	Residue	Details
G	ASP107-MET122

site_id	PS00018
Number of Residues	13
Details	EF_HAND_1 EF-hand calcium-binding domain. DIDAEKLMCpqEI

Chain	Residue	Details
G	ASP132-ILE144

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

Chain	Residue	Details
B	CYS111-PRO122
B	CYS150-PRO161

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

Chain	Residue	Details
Q	LEU116-LYS127

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

Chain	Residue	Details
P	GLU167-LEU188

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

Chain	Residue	Details
M	PRO61-CYS78

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

Chain	Residue	Details
M	CYS128-GLN140

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

Chain	Residue	Details
M	ARG175-PHE185

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

Chain	Residue	Details
A	GLY200-SER215

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

Chain	Residue	Details
A	GLU377-GLY388

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

Chain	Residue	Details
O	ASP166-PRO184

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

Chain	Residue	Details
C	GLY169-PRO185

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	65
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"28844695","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5XTB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q91YT0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q91YT0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"UniProtKB","id":"Q91YT0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	29
Details	Domain: {"description":"4Fe-4S ferredoxin-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00711","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	29
Details	Domain: {"description":"4Fe-4S ferredoxin-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00711","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00711","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	7
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Hydroxyarginine","evidences":[{"source":"PubMed","id":"27226634","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q9CQ75","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	75
Details	Domain: {"description":"Carrier","evidences":[{"source":"PROSITE-ProRule","id":"PRU00258","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9CR21","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"O-(pantetheine 4'-phosphoryl)serine","evidences":[{"source":"PROSITE-ProRule","id":"PRU00258","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"31664822","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6ODD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9CPP6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	1
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q9CPP6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	43
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9Z1P6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9DC69","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9DC69","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by PKA","evidences":[{"source":"PubMed","id":"20433953","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	78
Details	Domain: {"description":"2Fe-2S ferredoxin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00465","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	39
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_FI27
Number of Residues	56
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_FI28
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01184","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q91VD9","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P04394","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PDB","id":"5XTB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XTI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9D6J6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	1
Details	Modified residue: {"description":"Phosphotyrosine; by SRC","evidences":[{"source":"PubMed","id":"22823520","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	1
Details	Modified residue: {"description":"Symmetric dimethylarginine","evidences":[{"source":"PubMed","id":"24089531","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24838397","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P52503","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)