9gy6

Mycobacterial cytochrome bc1:aa3 with inhibitor

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome bc1 complex Rieske iron-sulfur subunit

Mycolicibacterium smegmatis MC2 155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R051_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–421； UniProt 2–408 Author chain M； PDBConstruct 15–421； UniProt 2–408

Cytochrome bc1 complex cytochrome b subunit

Mycolicibacterium smegmatis MC2 155

UniProt A0R052

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R052_MYCS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–546； UniProt 1–546 Author chain N； PDBConstruct 1–546； UniProt 1–546

Cytochrome bc1 complex cytochrome c subunit

Mycolicibacterium smegmatis MC2 155

UniProt A0R050

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R050_MYCS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–268； UniProt 1–268 Author chain O； PDBConstruct 1–268； UniProt 1–268

Transmembrane protein

Mycolicibacterium smegmatis MC2 155

UniProt A0QVH4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0QVH4_MYCS2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–84； UniProt 1–84 Author chain P； PDBConstruct 1–84； UniProt 1–84

Cytochrome c oxidase subunit 2

Mycolicibacterium smegmatis MC2 155

UniProt A0R057

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R057_MYCS2
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–341； UniProt 1–341 Author chain Q； PDBConstruct 1–341； UniProt 1–341

Cytochrome c oxidase subunit 1

Mycolicibacterium smegmatis MC2 155

UniProt A0A2U9PNL2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2U9PNL2_MYCSE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 21–575； UniProt 1–555 Author chain R； PDBConstruct 21–575； UniProt 1–555

Cytochrome c oxidase subunit 3

Mycolicibacterium smegmatis MC2 155

UniProt A0R049

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R049_MYCS2
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–203； UniProt 1–203 Author chain S； PDBConstruct 1–203； UniProt 1–203

Cytochrome c oxidase polypeptide 4

Mycolicibacterium smegmatis MC2 155

UniProt A0R056

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R056_MYCS2
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–139； UniProt 1–139 Author chain T； PDBConstruct 1–139； UniProt 1–139

Secreted protein

Mycolicibacterium smegmatis MC2 155

UniProt A0R1B6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） DUF5130 domain-containing protein × 2 （A0R1B5） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R1B6_MYCS2
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–79； UniProt 1–79 Author chain U； PDBConstruct 1–79； UniProt 1–79

DUF5130 domain-containing protein

Mycolicibacterium smegmatis MC2 155

UniProt A0R1B5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） Superoxide dismutase [Cu-Zn] × 2 （A0QQQ1） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y4692_MYCS2
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–157； UniProt 1–157 Author chain V； PDBConstruct 1–157； UniProt 1–157

Superoxide dismutase [Cu-Zn]

Mycolicibacterium smegmatis MC2 155

UniProt A0QQQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 22	Cytochrome bc1 complex Rieske iron-sulfur subunit × 2 （A0R051） Cytochrome bc1 complex cytochrome b subunit × 2 （A0R052） Cytochrome bc1 complex cytochrome c subunit × 2 （A0R050） Transmembrane protein × 2 （A0QVH4） Cytochrome c oxidase subunit 2 × 2 （A0R057） Cytochrome c oxidase subunit 1 × 2 （A0A2U9PNL2） Cytochrome c oxidase subunit 3 × 2 （A0R049） Cytochrome c oxidase polypeptide 4 × 2 （A0R056） Secreted protein × 2 （A0R1B6） DUF5130 domain-containing protein × 2 （A0R1B5） FE2/S2 (INORGANIC) CLUSTER × 2 ;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ; × 4 PALMITIC ACID × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 CARDIOLIPIN × 17 ;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ; × 2 HEME C × 4 MENAQUINONE-9 × 2 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 4 COPPER (II) ION × 8 HEME-A × 4 CALCIUM ION × 2 MENAQUINONE-7 × 2 water × 19	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0QQQ1_MYCS2
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain L； PDBConstruct 1–236； UniProt 1–236 Author chain X； PDBConstruct 1–236； UniProt 1–236

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9gy6
Deposition date deposition_date	2024-10-01
Structure title title	Mycobacterial cytochrome bc1:aa3 with inhibitor
Keywords keywords	membrane protein, inhibitor complex, mycobacterium, cytochrome bc, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9gy6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9gy6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gy6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	63.91 Å
Rg (electron density)	63.89 Å
Total Rg	63.66 Å
Atom count	43096
Residues	5206
Excluded volume	785460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gy6__assembly_1__model_1`	22-meric （22）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (25)

Entity 1 Entity 1 polymer

Description description	Cytochrome bc1 complex Rieske iron-sulfur subunit
Molecular weight formula_weight	46383.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,M
Atom count atom_count	43307

MDYRNGGRHRCGHVDRIASMSQDSPDIKGTDAPGQTGVPGQPTDAELAEMSREELVKLGGKIDGVETIFKEPRWPVPGTKAEKRTERLVAYWLMLGGLSGLALLLVFLFWPWEYQPFGSEGEFLYSLATPLYGLTFGLSILSIGIGAVLFQKKFIPEEISVQDRHDGRSPEVHRKTVAANLTDALEGSTLKRRKVIGLSLGIGLGAFGAGTLVAFIGGLIKNPWKPVVPTAEGKKAVLWTSGWTPRFKGETIYLARATGRPGESPFVKMRPEDIDAGGMETVFPWRESDGDGTTVESEHKLTEIAMGVRNPVMLIRIKPADMHRVIKRKGQESFNFGELFAYTKVCSHLGCPSSLYEQQTYRILCPCHQSQFDALEFAKPIFGPAARALAQLPITIDEDGYLVANGDFVEPVGPAFWERKS

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 Entity 2 polymer

Description description	Cytochrome bc1 complex cytochrome b subunit
Molecular weight formula_weight	60262.9 kDa
EC 编号 ec_number	7.1.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,N

MSPDFAKLAAAQGDAIDSRYHPSAAVRRQLNKVFPTHWSFLLGEIALYSFIILLLTGVWLTLFFDPSMAHVTYDGVYQPLRGVQMSRAYETALDISFEVRGGLFVRQVHHWAALMFAASIMVHLARIFFTGAFRRPREANWVIGSLLLILAMFEGYFGYSLPDDLLSGTGIRAALSGITMGMPVIGTWLHWALFGGDFPGEILIPRLYALHILLIPGIILALIGAHLALVWFQKHTQFPGPGRTETNVVGVRVMPVFAVKSGAFFAMITGVLGLMGGLLTINPIWNLGPYKPSQVSAGSQPDFYMMWTEGLARLWPAWEFYPFGHTIPQGVWVAVGMGLVFALLIAYPFIEKKVTGDDAHHNLLQRPRDVPVRTAIGSMAIALYLLLTFACMNDIIALKFHISLNATTWIGRIGMVVLPAIVYFVAYRWAISLQRSDREVLEHGVETGIIKRLPHGAYVELHQPLGPVDEHGHPIPLEYAGAPLPKRMNKLGSGGAPGTGSFLFPDPAVEHEALTEAAHASEHKSLTALKEHQDRIHGNGETNGHH

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 3 Entity 3 polymer

Description description	Cytochrome bc1 complex cytochrome c subunit
Molecular weight formula_weight	27874.5 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,O

MTSKSRRRLRRRLSAGLLLLIGLAVAGGVAATLTPQPQVAVADESQSALLRTGKQLFETSCVSCHGANLQGVPDRGPSLIGTGEAAVYFQVSTGRMPAMRGEAQAPSKPPHFDESQIDALGAYVQANGGGPTVPRDDHGAVAQESLIGGDVARGGDLFRLNCASCHNFTGKGGALSSGKYAPDLGDANPAQIYTAMLTGPQNMPKFSDRQLTPDEKRDIVAYVRESAETPSYGGYGLGGFGPAPEGMAMWIIGMVAAIGVAMWIGSRA

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 4 Entity 4 polymer

Description description	Transmembrane protein
Molecular weight formula_weight	9531.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,P

MANTEVERHTGVDVEDVPSAEWGWSHMPIGVMHIGGLLSAAFLLVMMRGNHVGHVEDWFLIGFAAVIVALVGRNWWLRRRGWIR

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 5 Entity 5 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	38077.5 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,Q

MTPRGFRVVALSIVLGGSALLLSGCSWSDALALGWPTGITPEAKLNRELWIGSVIASFAVGAIVWGLIFWTSAFHRKKATDTELPRQFGYNMPLELTLTVIPFLIISVLFYFTVVVQERMMHKDPNPEVVIDVTAFQWNWKFGYQKIAFADGSFDYDGADPERKEAMTSRPEGKDEHGIEKVGPIRGMTPEDRTYLNFDKIETLGTSSEIPVLVLPAGKRIEFVLNSADVIHGFWVPEFLFKRDVLPEPKANNSDNVFQVSEIQQTGAFVGRCTEMCGTFHAMMNFEVRVVEPNDFKAYIDQRNAGKTNAEALAAINQPPLAITTEPFESRRGELVPQASK

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 6 Entity 6 polymer

Description description	Cytochrome c oxidase subunit 1
Molecular weight formula_weight	64163.0 kDa
EC 编号 ec_number	7.1.1.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,R

MVAEAPPIGELEARRPFPERMGPKGNLIYKLITTTDHKLIGIMYCVVCFAFFLVGGLMALFMRTELAMPGLQFLSNEQFNQLFTMHGTVMLLFYATPIVFGFANLVLPLQIGAPDVAFPRLNALSFWLFLFGALIAIAGFITPGGAADFGWTAYSPLTDAIHSPGAGGDLWIMGLAVGGLGTILGGVNMITTVVCMRAPGMTMFRMPIFTWNILVTSILVLIAFPILTAALFGLAADRHLGAHIYDPANGGVLLWQHLFWFFGHPEVYIIALPFFGIVSEIFPVFSRKPIFGYTTLIYATLAIAALSVAVWAHHMYATGAVLLPFFSFMTFLIAVPTGIKFFNWIGTMWKGQLTFETPMLFSVGFLITFLLGGLSGVLLASPPLDFHVTDSYFVIAHFHYVLFGTIVFATYAGIYFWFPKMTGRLLDERLGKLHFWLTFIGFHTTFLVQHWLGDEGMPRRYADYLPTDGFTTLNVISTVGAFILGVSMLPFVWNVFKSWRYGEPVTVDDPWGYGNSLEWATSCPPPRHNFTELPRIRSERPAFELHYPHMVERMRAEAHVGRAHHPELETADKSS

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 7 Entity 7 polymer

Description description	Cytochrome c oxidase subunit 3
Molecular weight formula_weight	22196.9 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,S

MTSAVGTSGTAITSRVHSLNRPNMVSVGTIVWLSSELMFFAGLFAMYFTARAQAGGAWPPEPTELNLALAVPVTLVLIASSFTCQMGVFAAERGDVFGLRRWYVITFLMGLFFVLGQGYEYIHLVEHGTTIPGSAYGSVFYLATGFHGLHVIGGLVAFVLLLARTKMSKFTPAQATAAIVVSYYWHFVDIVWIALFATIYFVR

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 8 Entity 8 polymer

Description description	Cytochrome c oxidase polypeptide 4
Molecular weight formula_weight	15177.4 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,T

MHIEARLFEILTAFFALAAVVYAVLTAMFATGGVEWAGTTALVLTTGLTLITGTFFRFVARRLDTRPEDYEDAEISDGAGELGFFAPHSWWPILISLSFSTAAVGAALWLPWLIAAGVAFVITSVCGLVFEYYWGPEKH

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 9 Entity 9 polymer

Description description	Secreted protein
Molecular weight formula_weight	8365.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,U

MSTALTHGLIGGVPLVLFAVLALIFLTRKGPHPDTYKMSDPWTHAPILWAAEEPREHGHGGHGHDSHGVVIGGGASGKW

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 10 Entity 10 polymer

Description description	DUF5130 domain-containing protein
Molecular weight formula_weight	15911.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,V

MASGDIATVANAELDLPYGSALTSSGRISAVTEPGELSVHYPFPTMDLVVLDDALKYGSRAAKARFAVYIGPLGADTAATAREILANVPTPENAVLLAVSPDQRAIEVVYGADVKGRGIESAAPLGVSAAAASFKEGNLIDGLISAVRVMSAGVSPA

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 11 Entity 11 polymer

Description description	Superoxide dismutase [Cu-Zn]
Molecular weight formula_weight	23232.4 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,X

MLKPVSVAVLFATPVLALSACSPPGETASSEPGTTPAIWTGSPSPAAPSGEDHGGGHGAGAAGAGETLTAELKTADGTSVATADFQFADGFATVTIETTTPGRLTPGFHGVHIHSVGKCEANSVAPTGGAPGDFNSAGGHFQVSGHSGHPASGDLSSLQVRADGSGKLVTTTDAFTAEDLLDGAKTAIIIHEKADNFANIPPERYQQVNGAPGPDQTTMATGDAGSRVACGVISAG

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 12 Entity 12 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 non-polymer

Description description	;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ;
Molecular weight formula_weight	853.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 14 Entity 14 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 15 Entity 15 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 16 Entity 16 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 17 Entity 17 non-polymer

Description description	;6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide ;
Molecular weight formula_weight	541.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 18 Entity 18 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 19 Entity 19 non-polymer

Description description	MENAQUINONE-9
Molecular weight formula_weight	785.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 20 Entity 20 non-polymer

Description description	(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
Molecular weight formula_weight	718.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 21 Entity 21 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 22 Entity 22 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 23 Entity 23 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 24 Entity 24 non-polymer

Description description	MENAQUINONE-7
Molecular weight formula_weight	649.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 25 Entity 25 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	42000

Mycobacterial cytochrome bc1:aa3 with inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome bc1 complex Rieske iron-sulfur subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome bc1 complex cytochrome b subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome bc1 complex cytochrome c subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transmembrane protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c oxidase polypeptide 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Secreted protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DUF5130 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer