4U3F

Cytochrome bc1 complex from chicken with designed inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization

Hao, G.-F.Yang, S.-G.Huang, W.Wang, L.Shen, Y.-Q.Tu, W.-L.Li, H.Huang, L.-S.Wu, J.-W.Berry, E.A.Yang, G.-F.

(2015) Sci Rep 5


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
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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 
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
Find proteins for D0VX26 (Gallus gallus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, 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
Cytochrome b-c1 complex subunit 7F,
P [auth S]
110Gallus gallusMutation(s): 0 
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
Cytochrome b-c1 complex subunit 6H,
R [auth U]
77Gallus gallusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI,
S [auth V]
76Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ5ZLR5
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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
Find proteins for F1NC51 (Gallus gallus)
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DB [auth T],
GA [auth D],
LA [auth G],
ZA [auth Q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10
Query on U10

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RA [auth P],
Y [auth C]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PEE
Query on PEE

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BA [auth C]
CB [auth R]
DA [auth C]
EA [auth C]
JA [auth E]
BA [auth C],
CB [auth R],
DA [auth C],
EA [auth C],
JA [auth E],
KA [auth E],
MA [auth N],
NA [auth P],
TA [auth P],
U [auth A],
VA [auth P],
WA [auth P],
XA [auth P],
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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FA [auth D],
YA [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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OA [auth P],
PA [auth P],
V [auth C],
W [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Y52
Query on Y52

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QA [auth P],
X [auth C]
methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate
C20 H19 N O4 S2
OMGAIUZPUSZZME-LFIBNONCSA-N
BOG
Query on BOG

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AB [auth Q],
HA [auth D],
SA [auth P]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
MES
Query on MES

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AA [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
FES
Query on FES

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BB [auth R],
IA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL
Query on GOL

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CA [auth C],
UA [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
C,
M [auth P]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.251α = 90
b = 181.483β = 90
c = 239.631γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Omodel building
PHENIXmodel building
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.0: 2023-09-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary