3L74

Cytochrome BC1 complex from chicken with famoxadone bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN IA, K [auth N]446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2B, L [auth O]441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for D0VX29 (Gallus gallus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME BC, M [auth P]380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P18946 (Gallus gallus)
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Entity ID: 4
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIALE, O [auth R]196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q5ZLR5 (Gallus gallus)
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Entity ID: 6
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIIIH, R [auth U]77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALI, S [auth V]47Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence 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
Find proteins for D0VX27 (Gallus gallus)
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
DB [auth Q], IA [auth D], IB [auth T], NA [auth G]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ (Subject of Investigation/LOI)
Query on UQ

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UA [auth P], Z [auth C]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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AA [auth C], BA [auth C], OA [auth N], PA [auth N], U [auth A], VA [auth P]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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CB [auth Q], HA [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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QA [auth P], RA [auth P], W [auth C], X [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FMX (Subject of Investigation/LOI)
Query on FMX

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TA [auth P], Y [auth C]FAMOXADONE
C22 H18 N2 O4
PCCSBWNGDMYFCW-QFIPXVFZSA-N
 Ligand Interaction
BOG (Subject of Investigation/LOI)
Query on BOG

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EB [auth Q], FB [auth Q], GA [auth C], JA [auth D], KA [auth D], SA [auth P]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

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

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CA [auth C], WA [auth P]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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AB [auth P] , BB [auth P] , DA [auth C] , EA [auth C] , FA [auth C] , GB [auth Q] , MA [auth E] , V [auth A] , 
AB [auth P], BB [auth P], DA [auth C], EA [auth C], FA [auth C], GB [auth Q], MA [auth E], V [auth A], XA [auth P], YA [auth P], ZA [auth P]
Unknown ligand
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.893α = 90
b = 181.687β = 90
c = 240.75γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-12-28 
  • Released Date: 2010-02-02 
  • Deposition Author(s): Huang, L., Berry, E.A.

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: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary