Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4PD4

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004222	molecular_function	metalloendopeptidase activity
A	0005515	molecular_function	protein binding
A	0005739	cellular_component	mitochondrion
A	0005743	cellular_component	mitochondrial inner membrane
A	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
A	0006627	biological_process	protein processing involved in protein targeting to mitochondrion
A	0008121	molecular_function	quinol-cytochrome-c reductase activity
A	0009060	biological_process	aerobic respiration
A	0045275	cellular_component	respiratory chain complex III
A	0045333	biological_process	cellular respiration
A	0046872	molecular_function	metal ion binding
A	1902600	biological_process	proton transmembrane transport
B	0004222	molecular_function	metalloendopeptidase activity
B	0005515	molecular_function	protein binding
B	0005739	cellular_component	mitochondrion
B	0005743	cellular_component	mitochondrial inner membrane
B	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
B	0006508	biological_process	proteolysis
B	0008121	molecular_function	quinol-cytochrome-c reductase activity
B	0009060	biological_process	aerobic respiration
B	0016020	cellular_component	membrane
B	0030061	cellular_component	mitochondrial crista
B	0045275	cellular_component	respiratory chain complex III
B	0045333	biological_process	cellular respiration
B	0046872	molecular_function	metal ion binding
B	1902600	biological_process	proton transmembrane transport
C	0005739	cellular_component	mitochondrion
C	0005743	cellular_component	mitochondrial inner membrane
C	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
C	0008121	molecular_function	quinol-cytochrome-c reductase activity
C	0009055	molecular_function	electron transfer activity
C	0009060	biological_process	aerobic respiration
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0022904	biological_process	respiratory electron transport chain
C	0045275	cellular_component	respiratory chain complex III
C	0045333	biological_process	cellular respiration
C	0046872	molecular_function	metal ion binding
C	1902600	biological_process	proton transmembrane transport
D	0009055	molecular_function	electron transfer activity
D	0020037	molecular_function	heme binding
E	0008121	molecular_function	quinol-cytochrome-c reductase activity
E	0016020	cellular_component	membrane
E	0051537	molecular_function	2 iron, 2 sulfur cluster binding
F	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
G	0005739	cellular_component	mitochondrion
G	0005743	cellular_component	mitochondrial inner membrane
G	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
G	0008121	molecular_function	quinol-cytochrome-c reductase activity
G	0009060	biological_process	aerobic respiration
G	0016020	cellular_component	membrane
G	0034551	biological_process	mitochondrial respiratory chain complex III assembly
G	0045275	cellular_component	respiratory chain complex III
G	0045333	biological_process	cellular respiration
G	0099617	cellular_component	matrix side of mitochondrial inner membrane
G	1902600	biological_process	proton transmembrane transport
H	0005739	cellular_component	mitochondrion
H	0005743	cellular_component	mitochondrial inner membrane
H	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
H	0008121	molecular_function	quinol-cytochrome-c reductase activity
H	0009060	biological_process	aerobic respiration
H	0016020	cellular_component	membrane
H	0045275	cellular_component	respiratory chain complex III
H	0045333	biological_process	cellular respiration
H	1902600	biological_process	proton transmembrane transport
I	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
I	0045275	cellular_component	respiratory chain complex III
J	0002250	biological_process	adaptive immune response
J	0002376	biological_process	immune system process
J	0005576	cellular_component	extracellular region
J	0019814	cellular_component	immunoglobulin complex
K	0002250	biological_process	adaptive immune response
K	0002376	biological_process	immune system process
K	0005576	cellular_component	extracellular region
K	0005886	cellular_component	plasma membrane
K	0006955	biological_process	immune response
K	0019814	cellular_component	immunoglobulin complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	binding site for residue UMQ A 501

Chain	Residue
A	TRP427
I	ASN14
I	ALA15
I	VAL16
I	PHE17
I	VAL18
A	ASP428
A	SER453
A	MET454
A	MET455
A	ARG456
A	3PH502
E	TYR57
E	SER68

site_id	AC2
Number of Residues	5
Details	binding site for residue 3PH A 502

Chain	Residue
A	SER450
A	UMQ501
C	HIS222
C	ILE226
E	SER67

site_id	AC3
Number of Residues	18
Details	binding site for residue HEM C 4001

Chain	Residue
C	GLN43
C	ILE44
C	GLY47
C	ILE48
C	MET50
C	ALA51
C	ARG79
C	HIS82
C	ALA83
C	THR127
C	ALA128
C	GLY131
C	TYR132
C	VAL135
C	PHE180
C	HIS183
C	TYR184
C	PRO187

site_id	AC4
Number of Residues	18
Details	binding site for residue HEM C 4002

Chain	Residue
C	TRP30
C	GLY33
C	SER34
C	LEU36
C	HIS96
C	MET97
C	LYS99
C	SER105
C	LEU113
C	TRP114
C	GLY117
C	VAL118
C	ILE120
C	VAL194
C	HIS197
C	LEU201
C	SER206
C	SER207

site_id	AC5
Number of Residues	11
Details	binding site for residue AOQ C 4003

Chain	Residue
C	PHE129
C	MET139
C	GLY143
C	VAL146
C	ILE147
C	ILE269
C	PRO271
C	LEU275
C	TYR279
C	ILE299
E	HIS181

site_id	AC6
Number of Residues	8
Details	binding site for residue 3PE C 4004

Chain	Residue
C	PHE3
C	ASN7
C	TYR9
C	LEU10
C	THR112
C	ASN115
C	VAL116
C	HIS204

site_id	AC7
Number of Residues	11
Details	binding site for residue UQ6 C 4005

Chain	Residue
C	TYR16
C	GLN22
C	SER34
C	ILE48
C	LEU182
C	LEU185
C	ALA191
C	LEU201
C	SER206
C	MET221
C	ASP229

site_id	AC8
Number of Residues	9
Details	binding site for residue 3PH C 4006

Chain	Residue
C	TRP29
C	MET95
C	MET97
C	ALA98
C	TYR102
C	TYR103
C	LEU302
C	THR317
C	PHE333

site_id	AC9
Number of Residues	16
Details	binding site for residue HEM D 401

Chain	Residue
D	ALA172
D	PRO175
D	ILE180
D	ARG184
D	TYR190
D	ILE191
D	LEU195
D	PHE218
D	MET225
D	VAL228
D	VAL251
D	VAL100
D	CYS101
D	CYS104
D	HIS105
D	ASN169

site_id	AD1
Number of Residues	7
Details	binding site for residue FES E 301

Chain	Residue
E	CYS159
E	HIS161
E	LEU162
E	CYS178
E	CYS180
E	HIS181
E	SER183

site_id	AD2
Number of Residues	11
Details	binding site for residue 3PH E 302

Chain	Residue
C	ILE42
C	MET237
D	LEU269
D	LYS272
D	THR273
D	ILE276
E	GLY70
E	ALA71
E	SER73
E	THR74
E	THR77

Functional Information from PROSITE/UniProt

site_id	PS00143
Number of Residues	23
Details	INSULINASE Insulinase family, zinc-binding region signature. Ggsryatkd.GvAHLLNRFnFqNT

Chain	Residue	Details
B	GLY37-THR59

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17761666","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	81
Details	Topological domain: {"description":"Mitochondrial matrix","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8031140","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	183
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"10873857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3CX5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	104
Details	Topological domain: {"description":"Mitochondrial intermembrane","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8031140","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"10873857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1EZV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KB9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KYO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P84","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2IBZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CX5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PD4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P00157","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	200
Details	Topological domain: {"description":"Mitochondrial intermembrane","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9430684","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	117
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	12
Details	Topological domain: {"description":"Mitochondrial matrix","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9430684","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	153
Details	Domain: {"description":"Cytochrome c","evidences":[{"source":"PROSITE-ProRule","id":"PRU00433","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	37
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	9
Details	Compositional bias: {"description":"Acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Binding site: {"description":"covalent","evidences":[{"source":"PubMed","id":"10873857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1EZV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KYO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KYO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	1
Details	Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"10873857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1EZV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KYO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	81
Details	Topological domain: {"description":"Mitochondrial matrix","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	147
Details	Topological domain: {"description":"Mitochondrial intermembrane","evidences":[{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	91
Details	Domain: {"description":"Rieske","evidences":[{"source":"PROSITE-ProRule","id":"PRU00628","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	3
Details	Region: {"description":"Hinge","evidences":[{"source":"PubMed","id":"30598556","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10873857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11880631","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18390544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30598554","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1EZV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KB9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KYO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P84","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2IBZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CX5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PD4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	10
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	22
Details	Region: {"description":"Framework-1"}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	10
Details	Region: {"description":"Complementarity-determining-1"}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	14
Details	Region: {"description":"Framework-2"}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	6
Details	Region: {"description":"Complementarity-determining-2"}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	31
Details	Region: {"description":"Framework-3"}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	8
Details	Region: {"description":"Complementarity-determining-3"}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	1
Details	M-CSA 208

Chain	Residue	Details
E	HIS181	covalently attached, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, radical stabiliser
C	SER206	electrostatic stabiliser, hydrogen bond donor, radical stabiliser
C	LYS228	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, radical stabiliser
C	ASP229	electrostatic stabiliser, hydrogen bond acceptor, radical stabiliser
C	GLU272	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, radical stabiliser

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