4U3F

Cytochrome bc1 complex from chicken with designed inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2312 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
A, N
446Gallus gallusMutation(s): 0 
Gene Names: UQCRC1
Find proteins for F1NAC6 (Gallus gallus)
Go to Gene View: UQCRC1
Go to UniProtKB:  F1NAC6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
B, O
441Gallus gallusMutation(s): 0 
Gene Names: UQCRC2
Find proteins for F1P582 (Gallus gallus)
Go to Gene View: UQCRC2
Go to UniProtKB:  F1P582
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P18946 (Gallus gallus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P18946
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial cytochrome c1, heme protein
D, Q
241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX26 (Gallus gallus)
Go to UniProtKB:  D0VX26
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, R
196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
F, S
110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
Go to UniProtKB:  D0VX30
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
G, T
81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX32 (Gallus gallus)
Go to UniProtKB:  D0VX32
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6
H, U
77Gallus gallusMutation(s): 0 
Gene Names: UQCRH
Find proteins for D0VX28 (Gallus gallus)
Go to Gene View: UQCRH
Go to UniProtKB:  D0VX28
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
I, V
76Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein
J, W
61Gallus gallusMutation(s): 0 
Gene Names: UQCR10
Find proteins for F1NC51 (Gallus gallus)
Go to Gene View: UQCR10
Go to UniProtKB:  F1NC51
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download SDF File 
Download CCD File 
C, P
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
CDL
Query on CDL

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Download CCD File 
D, G, Q, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
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
HEC
Query on HEC

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Download CCD File 
D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
BOG
Query on BOG

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Download CCD File 
D, P, Q
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
PEE
Query on PEE

Download SDF File 
Download CCD File 
A, C, E, N, P, R
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
AME
Query on AME
I, V
NON-POLYMERC7 H13 N O3 S

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FME
Query on FME
C, P
L-PEPTIDE LINKINGC6 H11 N O3 SMET
UNK
Query on UNK
I, V
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2312 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 167.251α = 90.00
b = 181.483β = 90.00
c = 239.631γ = 90.00
Software Package:
Software NamePurpose
Omodel building
SCALEPACKdata scaling
PHENIXphasing
DENZOdata reduction
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description