3CWB

Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D

PDB DOI: https://doi.org/10.2210/pdb3CWB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gallus gallus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2008-04-21 Released: 2008-08-12
Deposition Author(s): Huang, L., Cromartie, T., Viner, R., Crowley, P.J., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.319
R-Value Work: 0.285
R-Value Observed: 0.285

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.

Crowley, P.J., Berry, E.A., Cromartie, T., Daldal, F., Godfrey, C.R., Lee, D.W., Phillips, J.E., Taylor, A., Viner, R.

(2008) Bioorg Med Chem 16: 10345-10355

PubMed: 18996700 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bmc.2008.10.030
Primary Citation of Related Structures:
3CWB

PubMed Abstract:
Extensive molecular modeling based on crystallographic data was used to aid the design of synthetic analogues of the fungicidal naturally occurring respiration inhibitors crocacins A and D, and an inhibitor binding model to the mammalian cytochrome bc(1) complex was constructed. Simplified analogues were made which showed high activity in a mitochondrial beef heart respiration assay, and which were also active against certain plant pathogens in glasshouse tests. A crystal structure was obtained of an analogue of crocacin D bound to the chicken heart cytochrome bc(1) complex, which validated the binding model and which confirmed that the crocacins are a new class of inhibitor of the cytochrome bc(1) complex.

Organizational Affiliation

Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG426EY, UK. patrick.crowley@syngenta.com

Macromolecule Content

Total Structure Weight: 481.9 kDa
Atom Count: 32,696
Modelled Residue Count: 4,078
Deposited Residue Count: 4,170
Unique protein chains: 10

Macromolecules

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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
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
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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
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
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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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN	E, O [auth R]	196	Gallus gallus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q5ZLR5 (Gallus gallus) Explore Q5ZLR5 Go to UniProtKB: Q5ZLR5
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UniProt Group	Q5ZLR5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN	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
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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 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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII	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
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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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence	I, S [auth V]	52	Gallus gallus	Mutation(s): 0 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: 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 Membrane Entity: Yes
UniProt
Find proteins for D0VX27 (Gallus gallus) Explore D0VX27 Go to UniProtKB: D0VX27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX27
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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 FA [auth D] SDF format, chain QA [auth P] SDF format, chain RA [auth P] SDF format, chain JA [auth G] MOL2 format, chain FA [auth D] MOL2 format, chain QA [auth P] MOL2 format, chain RA [auth P] MOL2 format, chain JA [auth G]	FA [auth D], JA [auth G], QA [auth P], RA [auth P]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain FA [auth D] Focus chain JA [auth G] Focus chain QA [auth P] Focus chain RA [auth P] Interactions & Density Focus chain FA [auth D] Focus chain JA [auth G] Focus chain QA [auth P] Focus chain RA [auth P]
UQ Query on UQ Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain PA [auth P] MOL2 format, chain AA [auth C] MOL2 format, chain PA [auth P]	AA [auth C], PA [auth P]	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-RECDIHICSA-N		Interactions Focus chain AA [auth C] Focus chain PA [auth P] Interactions & Density Focus chain AA [auth C] Focus chain PA [auth P]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain SA [auth P] SDF format, chain TA [auth P] SDF format, chain U [auth A] SDF format, chain BB [auth W] SDF format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain SA [auth P] MOL2 format, chain TA [auth P] MOL2 format, chain U [auth A] MOL2 format, chain BB [auth W] MOL2 format, chain CA [auth C]	BA [auth C] BB [auth W] CA [auth C] SA [auth P] TA [auth P] BA [auth C], BB [auth W], CA [auth C], SA [auth P], TA [auth P], U [auth A]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain BA [auth C] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain SA [auth P] Focus chain TA [auth P] Focus chain U [auth A] Interactions & Density Focus chain BA [auth C] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain SA [auth P] Focus chain TA [auth P] Focus chain U [auth A]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain YA [auth Q] MOL2 format, chain EA [auth D] MOL2 format, chain YA [auth Q]	EA [auth D], YA [auth Q]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain EA [auth D] Focus chain YA [auth Q] Interactions & Density Focus chain EA [auth D] Focus chain YA [auth Q]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain MA [auth P] SDF format, chain NA [auth P] SDF format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain MA [auth P] MOL2 format, chain NA [auth P] MOL2 format, chain Y [auth C]	MA [auth P], NA [auth P], X [auth C], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain MA [auth P] Focus chain NA [auth P] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain MA [auth P] Focus chain NA [auth P] Focus chain X [auth C] Focus chain Y [auth C]
ICX Query on ICX Download Ideal Coordinates CCD File SDF format, chain OA [auth P] SDF format, chain Z [auth C] MOL2 format, chain OA [auth P] MOL2 format, chain Z [auth C]	OA [auth P], Z [auth C]	methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate C₂₃ H₂₅ I N₂ O₄ GJXNVOLPXGNHOU-CPSFFCFKSA-N		Interactions Focus chain OA [auth P] Focus chain Z [auth C] Interactions & Density Focus chain OA [auth P] Focus chain Z [auth C]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain KA [auth P] SDF format, chain V [auth C] SDF format, chain WA [auth Q] SDF format, chain XA [auth Q] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth Q] MOL2 format, chain XA [auth Q]	DA [auth D] GA [auth E] KA [auth P] V [auth C] WA [auth Q] DA [auth D], GA [auth E], KA [auth P], V [auth C], WA [auth Q], XA [auth Q]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain DA [auth D] Focus chain GA [auth E] Focus chain KA [auth P] Focus chain V [auth C] Focus chain WA [auth Q] Focus chain XA [auth Q] Interactions & Density Focus chain DA [auth D] Focus chain GA [auth E] Focus chain KA [auth P] Focus chain V [auth C] Focus chain WA [auth Q] Focus chain XA [auth Q]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain AB [auth R] SDF format, chain HA [auth E] MOL2 format, chain AB [auth R] MOL2 format, chain HA [auth E]	AB [auth R], HA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AB [auth R] Focus chain HA [auth E] Interactions & Density Focus chain AB [auth R] Focus chain HA [auth E]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain LA [auth P] SDF format, chain W [auth C] MOL2 format, chain LA [auth P] MOL2 format, chain W [auth C]	LA [auth P], W [auth C]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain LA [auth P] Focus chain W [auth C] Interactions & Density Focus chain LA [auth P] Focus chain W [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	IA [auth E], UA [auth P], VA [auth P], ZA [auth Q]	Unknown ligand IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain ZA [auth Q] Interactions & Density Focus chain IA [auth E] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain ZA [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.319
R-Value Work: 0.285
R-Value Observed: 0.285
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.778	α = 90
b = 182.663	β = 90
c = 242.945	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2014-10-29
Changes: Non-polymer description
Version 1.3: 2017-10-25
Changes: Advisory, Refinement description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.0: 2023-08-30
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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Help and Resources

3CWB

Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D

The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.

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

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

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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)