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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 b ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
A, N
446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX31 (Gallus gallus)
Go to UniProtKB:  D0VX31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
B, O
441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX29 (Gallus gallus)
Go to UniProtKB:  D0VX29
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P18946 (Gallus gallus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P18946
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
D, Q
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN
E, R
196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
F, S
110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
Go to UniProtKB:  D0VX30
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
G, T
81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX32 (Gallus gallus)
Go to UniProtKB:  D0VX32
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
H, U
77Gallus gallusMutation(s): 0 
Find proteins for D0VX28 (Gallus gallus)
Go to UniProtKB:  D0VX28
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence
I, V
52Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
J, W
61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX27 (Gallus gallus)
Go to UniProtKB:  D0VX27
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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D, G, P
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
AZI
Query on AZI

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

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

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Download CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

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

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

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C, D, E, P, Q
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
PEE
Query on PEE

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Download CCD File 
A, C, P, W
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
I, V
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.285 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 174.778α = 90.00
b = 182.663β = 90.00
c = 242.945γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
Blu-Icedata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2014-10-29
    Type: Non-polymer description
  • Version 1.3: 2017-10-25
    Type: Advisory, Refinement description