3L75

Cytochrome BC1 complex from chicken with fenamidone bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Go to UniProtKB:  D0VX31
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
Find proteins for D0VX29 (Gallus gallus)
Explore D0VX29 
Go to UniProtKB:  D0VX29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VX29
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME BC,
M [auth P]		380Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P18946 (Gallus gallus)
Explore P18946 
Go to UniProtKB:  P18946
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18946
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIND,
N [auth Q]		241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for D0VX26 (Gallus gallus)
Go to UniProtKB:  D0VX26
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for Q5ZLR5 (Gallus gallus)
Go to UniProtKB:  Q5ZLR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for D0VX30 (Gallus gallus)
Go to UniProtKB:  D0VX30
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for D0VX32 (Gallus gallus)
Go to UniProtKB:  D0VX32
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for D0VX28 (Gallus gallus)
Go to UniProtKB:  D0VX28
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for Q5ZLR5 (Gallus gallus)
Go to UniProtKB:  Q5ZLR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
UniProt
Find proteins for D0VX27 (Gallus gallus)
Go to UniProtKB:  D0VX27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
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
UQ
Query on UQ
Download Ideal Coordinates CCD File 
TA [auth P],
Z [auth C]		Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
PEE
Query on PEE
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
OA [auth N]
U [auth A]
UA [auth P]
AA [auth C],
BA [auth C],
OA [auth N],
U [auth A],
UA [auth P],
VA [auth P]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC
Download Ideal Coordinates CCD File 
CB [auth Q],
HA [auth D]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
Download Ideal Coordinates CCD File 
PA [auth P],
QA [auth P],
W [auth C],
X [auth C]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FNM
Query on FNM
Download Ideal Coordinates CCD File 
SA [auth P],
Y [auth C]		(5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one
C17 H17 N3 O S
LMVPQMGRYSRMIW-KRWDZBQOSA-N
BOG
Query on BOG
Download Ideal Coordinates CCD File 
EB [auth Q]
FB [auth Q]
GA [auth C]
JA [auth D]
KA [auth D]
EB [auth Q],
FB [auth Q],
GA [auth C],
JA [auth D],
KA [auth D],
RA [auth P]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES
Query on FES
Download Ideal Coordinates CCD File 
GB [auth R],
MA [auth E]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
AZI
Query on AZI
Download Ideal Coordinates CCD File 
CA [auth C],
WA [auth P]		AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
UNL
Query on UNL
Download Ideal Coordinates CCD File 
AB [auth P]
BB [auth P]
DA [auth C]
EA [auth C]
FA [auth C]
AB [auth P],
BB [auth P],
DA [auth C],
EA [auth C],
FA [auth C],
HB [auth R],
LA [auth D],
V [auth A],
XA [auth P],
YA [auth P],
ZA [auth P]
Unknown ligand
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.285α = 90
b = 182.141β = 90
c = 241.198γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2018-02-14
    Changes: Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, 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