6ZFU

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor RKA066

PDB DOI: https://doi.org/10.2210/pdb6ZFU/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2020-06-17 Released: 2021-06-30
Deposition Author(s): Amporndanai, K., O'Neill, P.M., Hong, W.D., Amewu, R.K., Pidathala, C., Berry, N.G., Biagini, G.A., Leung, S.C., Hasnain, S.S., Antonyuk, S.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.238
R-Value Work: 0.221
R-Value Observed: 0.222

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials

Amporndanai, K., O'Neill, P.M., Hong, W.D., Amewu, R.K., Pidathala, C., Berry, N., Biangini, G.A., Leung, S.C., Hasnain, S.S., Antonyuk, S.V.

To be published.

Macromolecule Content

Total Structure Weight: 237.96 kDa
Atom Count: 16,290
Modelled Residue Count: 2,015
Deposited Residue Count: 2,020
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A	444	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P31800 (Bos taurus) Explore P31800 Go to UniProtKB: P31800
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31800
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B	420	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P23004 (Bos taurus) Explore P23004 Go to UniProtKB: P23004
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23004
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C	378	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00157 (Bos taurus) Explore P00157 Go to UniProtKB: P00157
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00157
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D	239	Bos taurus	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00125 (Bos taurus) Explore P00125 Go to UniProtKB: P00125
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00125
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E	196	Bos taurus	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272 Go to UniProtKB: P13272
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13272
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F	99	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00129 (Bos taurus) Explore P00129 Go to UniProtKB: P00129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00129
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G	74	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13271 (Bos taurus) Explore P13271 Go to UniProtKB: P13271
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13271
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H	65	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00126 (Bos taurus) Explore P00126 Go to UniProtKB: P00126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00126
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I	46	Bos taurus	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272 Go to UniProtKB: P13272
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13272
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J	59	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00130 (Bos taurus) Explore P00130 Go to UniProtKB: P00130
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00130
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain M [auth A] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	BA [auth E], M [auth A], S [auth C], X [auth D]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BA [auth E] Focus chain M [auth A] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain M [auth A] Focus chain S [auth C] Focus chain X [auth D]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain AA [auth E] MOL2 format, chain T [auth C] MOL2 format, chain AA [auth E] mmCIF format, chain T [auth C] mmCIF format, chain AA [auth E]	AA [auth E], T [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AA [auth E] Focus chain T [auth C] Interactions & Density Focus chain AA [auth E] Focus chain T [auth C]
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	N [auth C], O [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain N [auth C] Focus chain O [auth C]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
JHE (Subject of Investigation/LOI) Query on JHE Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	3-methyl-1-oxidanyl-2-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]quinolin-4-one C₂₄ H₁₈ F₃ N O₃ ZSBSILZBHTWRSX-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
6PE Query on 6PE Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C₁₇ H₃₃ N O₈ P PELYUHWUVHDSSU-OAHLLOKOSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	K [auth A], Q [auth C], R [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain Y [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain Y [auth E]	Y [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain Y [auth E] Interactions & Density Focus chain Y [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain W [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain W [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain W [auth D]	CA [auth F], DA [auth G], EA [auth G], FA [auth G], W [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain W [auth D] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.238
R-Value Work: 0.221
R-Value Observed: 0.222
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.74	α = 90
b = 210.74	β = 90
c = 343.935	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 2.0: 2024-01-24
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary

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Help and Resources

6ZFU

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor RKA066

Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)