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


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 iAN446Gallus gallusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
Find proteins for F1NAC6 (Gallus gallus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2BO441Gallus gallusMutation(s): 0 
Gene Names: UQCRC2
EC: 1.10.2.2
Find proteins for F1P582 (Gallus gallus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bCP380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Find proteins for P18946 (Gallus gallus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial cytochrome c1, heme proteinDQ241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX26 (Gallus gallus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialER196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for Q5ZLR5 (Gallus gallus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7FS110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-cGT81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX32 (Gallus gallus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6HU77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
Find proteins for D0VX28 (Gallus gallus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialIV76Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for Q5ZLR5 (Gallus gallus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda proteinJW61Gallus gallusMutation(s): 0 
Gene Names: UQCR10
EC: 1.10.2.2
Find proteins for F1NC51 (Gallus gallus)
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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D, G, Q, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
U10
Query on U10

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C, P
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
PEE
Query on PEE

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A, C, E, N, P, R
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
HEC
Query on HEC

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D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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C, P
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Y52
Query on Y52

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C, P
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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D, P, Q
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
MES
Query on MES

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

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

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C, P
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C,PL-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



Entry History 

Deposition Data

Revision History 

  • 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