4U3F | pdb_00004u3f

Cytochrome bc1 complex from chicken with designed inhibitor bound

PDB DOI: https://doi.org/10.2210/pdb4U3F/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Gallus gallus
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2014-07-21 Released: 2015-07-29
Deposition Author(s): Huang, L.-S., Zhu, X.-L., Yang, G.F., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.23 Å
R-Value Free:
0.284 (Depositor), 0.289 (DCC)
R-Value Work:
0.236 (Depositor), 0.246 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization

Hao, G.-F., Yang, S.-G., Huang, W., Wang, L., Shen, Y.-Q., Tu, W.-L., Li, H., Huang, L.-S., Wu, J.-W., Berry, E.A., Yang, G.-F.

(2015) Sci Rep 5

DOI: https://doi.org/10.1038/srep13471

Macromolecule Content

Total Structure Weight: 492.11 kDa
Atom Count: 32,790
Modeled Residue Count: 4,065
Deposited Residue Count: 4,218
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i	A, K [auth N]	446	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX31 (Gallus gallus) Explore D0VX31 Go to UniProtKB: D0VX31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX31
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2	B, L [auth O]	441	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX29 (Gallus gallus) Explore D0VX29 Go to UniProtKB: D0VX29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX29
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C, M [auth P]	380	Gallus gallus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P18946 (Gallus gallus) Explore P18946 Go to UniProtKB: P18946
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18946
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial cytochrome c1, heme protein	D, N [auth Q]	241	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX26 (Gallus gallus) Explore D0VX26 Go to UniProtKB: D0VX26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX26
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E, O [auth R]	196	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZLR5
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F, P [auth S]	110	Gallus gallus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VX30 (Gallus gallus) Explore D0VX30 Go to UniProtKB: D0VX30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX30
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c	G, Q [auth T]	81	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for D0VX32 (Gallus gallus) Explore D0VX32 Go to UniProtKB: D0VX32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX32
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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	H, R [auth U]	77	Gallus gallus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VX28 (Gallus gallus) Explore D0VX28 Go to UniProtKB: D0VX28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX28
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I, S [auth V]	76	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZLR5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein	J, T [auth W]	61	Gallus gallus	Mutation(s): 0 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for F1NC51 (Gallus gallus) Explore F1NC51 Go to UniProtKB: F1NC51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1NC51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain DB [auth T] SDF format, chain LA [auth G] SDF format, chain ZA [auth Q] SDF format, chain GA [auth D] MOL2 format, chain DB [auth T] MOL2 format, chain LA [auth G] MOL2 format, chain ZA [auth Q] MOL2 format, chain GA [auth D] mmCIF format, chain DB [auth T] mmCIF format, chain LA [auth G] mmCIF format, chain ZA [auth Q] mmCIF format, chain GA [auth D]	DB [auth T], GA [auth D], LA [auth G], ZA [auth Q]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DB [auth T] Focus chain GA [auth D] Focus chain LA [auth G] Focus chain ZA [auth Q] Interactions & Density Focus chain DB [auth T] Focus chain GA [auth D] Focus chain LA [auth G] Focus chain ZA [auth Q]
U10 Query on U10 Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain RA [auth P] MOL2 format, chain Y [auth C] MOL2 format, chain RA [auth P] mmCIF format, chain Y [auth C] mmCIF format, chain RA [auth P]	RA [auth P], Y [auth C]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain RA [auth P] Focus chain Y [auth C] Interactions & Density Focus chain RA [auth P] Focus chain Y [auth C]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth R] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain KA [auth E] SDF format, chain MA [auth N] SDF format, chain NA [auth P] SDF format, chain TA [auth P] SDF format, chain U [auth A] SDF format, chain VA [auth P] SDF format, chain WA [auth P] SDF format, chain XA [auth P] SDF format, chain Z [auth C] SDF format, chain JA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth R] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth P] MOL2 format, chain TA [auth P] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth P] MOL2 format, chain WA [auth P] MOL2 format, chain XA [auth P] MOL2 format, chain Z [auth C] MOL2 format, chain JA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth R] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth P] mmCIF format, chain TA [auth P] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth P] mmCIF format, chain WA [auth P] mmCIF format, chain XA [auth P] mmCIF format, chain Z [auth C] mmCIF format, chain JA [auth E]	BA [auth C] CB [auth R] DA [auth C] EA [auth C] JA [auth E] BA [auth C], CB [auth R], DA [auth C], EA [auth C], JA [auth E], KA [auth E], MA [auth N], NA [auth P], TA [auth P], U [auth A], VA [auth P], WA [auth P], XA [auth P], Z [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth R] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth N] Focus chain NA [auth P] Focus chain TA [auth P] Focus chain U [auth A] Focus chain VA [auth P] Focus chain WA [auth P] Focus chain XA [auth P] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth R] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth N] Focus chain NA [auth P] Focus chain TA [auth P] Focus chain U [auth A] Focus chain VA [auth P] Focus chain WA [auth P] Focus chain XA [auth P] Focus chain Z [auth C]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain YA [auth Q] SDF format, chain FA [auth D] MOL2 format, chain YA [auth Q] MOL2 format, chain FA [auth D] mmCIF format, chain YA [auth Q] mmCIF format, chain FA [auth D]	FA [auth D], YA [auth Q]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain FA [auth D] Focus chain YA [auth Q] Interactions & Density Focus chain FA [auth D] Focus chain YA [auth Q]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain PA [auth P] SDF format, chain OA [auth P] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain PA [auth P] MOL2 format, chain OA [auth P] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain PA [auth P] mmCIF format, chain OA [auth P]	OA [auth P], PA [auth P], V [auth C], W [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain OA [auth P] Focus chain PA [auth P] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain OA [auth P] Focus chain PA [auth P] Focus chain V [auth C] Focus chain W [auth C]
Y52 Query on Y52 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain QA [auth P] MOL2 format, chain X [auth C] MOL2 format, chain QA [auth P] mmCIF format, chain X [auth C] mmCIF format, chain QA [auth P]	QA [auth P], X [auth C]	methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate C₂₀ H₁₉ N O₄ S₂ OMGAIUZPUSZZME-LFIBNONCSA-N		Interactions Focus chain QA [auth P] Focus chain X [auth C] Interactions & Density Focus chain QA [auth P] Focus chain X [auth C]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain SA [auth P] SDF format, chain HA [auth D] SDF format, chain AB [auth Q] MOL2 format, chain SA [auth P] MOL2 format, chain HA [auth D] MOL2 format, chain AB [auth Q] mmCIF format, chain SA [auth P] mmCIF format, chain HA [auth D] mmCIF format, chain AB [auth Q]	AB [auth Q], HA [auth D], SA [auth P]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain AB [auth Q] Focus chain HA [auth D] Focus chain SA [auth P] Interactions & Density Focus chain AB [auth Q] Focus chain HA [auth D] Focus chain SA [auth P]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AA [auth C]	AA [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain BB [auth R] MOL2 format, chain IA [auth E] MOL2 format, chain BB [auth R] mmCIF format, chain IA [auth E] mmCIF format, chain BB [auth R]	BB [auth R], IA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain BB [auth R] Focus chain IA [auth E] Interactions & Density Focus chain BB [auth R] Focus chain IA [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain UA [auth P] SDF format, chain CA [auth C] MOL2 format, chain UA [auth P] MOL2 format, chain CA [auth C] mmCIF format, chain UA [auth P] mmCIF format, chain CA [auth C]	CA [auth C], UA [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain UA [auth P] Interactions & Density Focus chain CA [auth C] Focus chain UA [auth P]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	C, M [auth P]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
UNK Query on UNK	I, S [auth V]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.23 Å
R-Value Free: 0.284 (Depositor), 0.289 (DCC)
R-Value Work: 0.236 (Depositor), 0.246 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.251	α = 90
b = 181.483	β = 90
c = 239.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
O	model building
PHENIX	model building
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2016-10-26
Changes: Database references
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.0: 2023-09-27
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4U3F | pdb_00004u3f

Cytochrome bc1 complex from chicken with designed inhibitor bound

Literature

Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization

Biological Assembly 1

Macromolecules

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

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)