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 OPMPDBTMMemProtMD

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 ?
R-Value Free:
0.284 (Depositor), 0.290 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

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

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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(by identity cutoff) | 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
UniProt
Find proteins for D0VX31 (Gallus gallus) Explore D0VX31 Go to UniProtKB: D0VX31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX31
Sequence Annotations Expand
Reference Sequence

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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
UniProt
Find proteins for D0VX29 (Gallus gallus) Explore D0VX29 Go to UniProtKB: D0VX29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX29
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18946
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX26
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZLR5
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX28
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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, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZLR5
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 RA [auth P] SDF format, chain Y [auth C] MOL2 format, chain RA [auth P] MOL2 format, chain Y [auth C] mmCIF format, chain RA [auth P] mmCIF format, chain Y [auth C]	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 JA [auth E] 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] 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 JA [auth E] 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] 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 JA [auth E] 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]	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 FA [auth D] SDF format, chain YA [auth Q] MOL2 format, chain FA [auth D] MOL2 format, chain YA [auth Q] mmCIF format, chain FA [auth D] mmCIF format, chain YA [auth Q]	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 PA [auth P] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain OA [auth P] MOL2 format, chain PA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain OA [auth P] mmCIF format, chain PA [auth P] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] 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 QA [auth P] SDF format, chain X [auth C] MOL2 format, chain QA [auth P] MOL2 format, chain X [auth C] mmCIF format, chain QA [auth P] mmCIF format, chain X [auth C]	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 AB [auth Q] SDF format, chain HA [auth D] SDF format, chain SA [auth P] MOL2 format, chain AB [auth Q] MOL2 format, chain HA [auth D] MOL2 format, chain SA [auth P] mmCIF format, chain AB [auth Q] mmCIF format, chain HA [auth D] mmCIF format, chain SA [auth P]	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 BB [auth R] SDF format, chain IA [auth E] MOL2 format, chain BB [auth R] MOL2 format, chain IA [auth E] mmCIF format, chain BB [auth R] mmCIF format, chain IA [auth E]	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 CA [auth C] SDF format, chain UA [auth P] MOL2 format, chain CA [auth C] MOL2 format, chain UA [auth P] mmCIF format, chain CA [auth C] mmCIF format, chain UA [auth P]	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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.23 ?
R-Value Free: 0.284 (Depositor), 0.290 (DCC)
R-Value Work: 0.236 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	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

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

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 4U3F | pdb_00004u3f

Cytochrome bc1 complex from chicken with designed inhibitor bound

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

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)

4U3F | pdb_00004u3f