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
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I A, N446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX31 (Gallus gallus)
Explore D0VX31 
Go to UniProtKB:  D0VX31
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2 B, O441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX29 (Gallus gallus)
Explore D0VX29 
Go to UniProtKB:  D0VX29
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b C, P380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB, COB, CYTB, MTCYB
Find proteins for P18946 (Gallus gallus)
Explore P18946 
Go to UniProtKB:  P18946
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN D, Q241Gallus gallusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN E, R196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1, RCJMB04_5b19
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Explore Q5ZLR5 
Go to UniProtKB:  Q5ZLR5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN F, S110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
Explore D0VX30 
Go to UniProtKB:  D0VX30
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C G, T81Gallus gallusMutation(s): 0 
Find proteins for D0VX32 (Gallus gallus)
Explore D0VX32 
Go to UniProtKB:  D0VX32
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII H, U77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
Find proteins for D0VX28 (Gallus gallus)
Explore D0VX28 
Go to UniProtKB:  D0VX28
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence I, V52Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1, RCJMB04_5b19
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Explore Q5ZLR5 
Go to UniProtKB:  Q5ZLR5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN J, W61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX27 (Gallus gallus)
Explore D0VX27 
Go to UniProtKB:  D0VX27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
Download Ideal Coordinates CCD File 
D, G, P
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L		 Ligand Interaction
UQ
Query on UQ
Download Ideal Coordinates CCD File 
C, P
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N		 Ligand Interaction
PEE
Query on PEE
Download Ideal Coordinates CCD File 
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
Download Ideal Coordinates CCD File 
D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
ICX
Query on ICX
Download Ideal Coordinates CCD File 
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
Download Ideal Coordinates CCD File 
C, D, E, P, Q
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
AZI
Query on AZI
Download Ideal Coordinates CCD File 
C, P
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
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


View more in-depth experimental data

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