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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein iA,
K [auth N]
446Gallus gallusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
UniProt
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UniProt GroupF1NAC6
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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 
Gene Names: UQCRC2
EC: 1.10.2.2
UniProt
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UniProt GroupF1P582
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC,
M [auth P]
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
UniProt
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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 Rieske, 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
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Entity ID: 6
MoleculeChainsSequence 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
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
Cytochrome b-c1 complex subunit 6H,
R [auth U]
77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI,
S [auth V]
76Gallus 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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UniProt GroupQ5ZLR5
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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 
Gene Names: UQCR10
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 10 Unique
IDChainsName / 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
 Ligand Interaction
U10
Query on U10

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

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FA [auth D],
YA [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
MES
Query on MES

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

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

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CA [auth C],
UA [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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

View Full Validation Report



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