3CWB

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


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


This is version 1.4 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

  • DOI: 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) ...

    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.


    Related Citations: 
    • Electron transfer by domain movement in cytochrome bc1.
      Zhang, Z., Huang, L., Shulmeister, V.M., Chi, Y.I., Kim, K.K., Hung, L.W., Crofts, A.R., Berry, E.A., Kim, S.H.
      (1998) Nature 392: 677
    • Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.
      Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.
      (2005) J Mol Biol 351: 573

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I AN446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX31 (Gallus gallus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2 BO441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX29 (Gallus gallus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b CP380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Find proteins for P18946 (Gallus gallus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN DQ241Gallus gallusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN ER196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 7.1.1.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN FS110Gallus gallusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C GT81Gallus gallusMutation(s): 0 
Find proteins for D0VX32 (Gallus gallus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII HU77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence IV52Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN JW61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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D, G, P
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ
Query on UQ

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C, P
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
PEE
Query on PEE

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A, C, P, W
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
HEC
Query on HEC

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D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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C, P
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ICX
Query on ICX

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C, P
methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate
C23 H25 I N2 O4
GJXNVOLPXGNHOU-CPSFFCFKSA-N
 Ligand Interaction
BOG
Query on BOG

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C, D, E, P, Q
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

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E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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C, P
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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E, P, Q
Unknown ligand
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
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 = 174.778α = 90
b = 182.663β = 90
c = 242.945γ = 90
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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