5OKD

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery.

Amporndanai, K.Johnson, R.M.O'Neill, P.M.Fishwick, C.W.G.Jamson, A.H.Rawson, S.Muench, S.P.Hasnain, S.S.Antonyuk, S.V.

(2018) IUCrJ 5: 200-210

  • DOI: 10.1107/S2052252518001616
  • Primary Citation of Related Structures:  
    6FO0, 6FO2, 6FO6, 5OKD

  • PubMed Abstract: 
  • Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochr ...

    Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc 1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.


    Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England.



Macromolecules
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD325Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G82Bos taurusMutation(s): 0 
Gene Names: UQCRQ
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH91Bos taurusMutation(s): 0 
Gene Names: UQCRH
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI47Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J64Bos taurusMutation(s): 0 
Gene Names: UQCR10
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA480Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Find proteins for P31800 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F111Bos taurusMutation(s): 0 
Gene Names: UQCRB
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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C, D, E
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PEE
Query on PEE

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C, E
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
PX4
Query on PX4

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E
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
HEC
Query on HEC

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

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

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C
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
9XE
Query on 9XE

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C
7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one
C23 H17 F3 N2 O3
ZZCQNODHORIHJA-UHFFFAOYSA-N
 Ligand Interaction
6PE
Query on 6PE

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A
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
 Ligand Interaction
PG4
Query on PG4

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A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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D, E, F, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.871α = 90
b = 209.871β = 90
c = 342.097γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references, Structure summary