3L72

Chicken cytochrome BC1 complex with kresoxim-I-dimethyl bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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


Literature

Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors.

Huang, L., Berry, E.A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN IA,
K [auth N]		446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for D0VX31 (Gallus gallus)
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UniProt GroupD0VX31
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2B,
L [auth O]		441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME BC,
M [auth P]		380Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIND,
N [auth Q]		241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIALE,
O [auth R]		196Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEINF,
P [auth S]		110Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-CG,
Q [auth T]		81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIIIH,
R [auth U]		77Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALI,
S [auth V]		47Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEINJ,
T [auth W]		61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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DA [auth D],
NA [auth P],
SA [auth Q],
Y [auth C]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ
Query on UQ
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MA [auth P],
X [auth C]		Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
PEE
Query on PEE
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AA [auth C]
HA [auth E]
OA [auth P]
PA [auth P]
WA [auth R]
AA [auth C],
HA [auth E],
OA [auth P],
PA [auth P],
WA [auth R],
Z [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC
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CA [auth D],
RA [auth Q]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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IA [auth P],
JA [auth P],
U [auth C],
V [auth C]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
IKR
Query on IKR
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LA [auth P],
W [auth C]		methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate
C19 H20 I N O4
QNSHGJNFUSNVMK-DYTRJAOYSA-N
BOG
Query on BOG
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EA [auth D],
FA [auth D],
KA [auth P],
TA [auth Q],
UA [auth Q]		octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES
Query on FES
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GA [auth E],
VA [auth R]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL
Query on GOL
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BA [auth C],
QA [auth P]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.614α = 90
b = 181.548β = 90
c = 241.033γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-10-29
    Changes: Non-polymer description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-05-05
    Changes: Structure summary
  • Version 2.0: 2023-09-06
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary