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 iA, K [auth N]446Gallus gallusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
UniProt
Find proteins for F1NAC6 (Gallus gallus)
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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
Find proteins for F1P582 (Gallus gallus)
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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
Find proteins for Q5ZLR5 (Gallus gallus)
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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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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
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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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] , KA [auth E] , MA [auth N] , NA [auth P] , 
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 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 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



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