6ZFS

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor WDH-1U-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials

Amporndanai, K.O'Neill, P.M.Hong, W.D.Amewu, R.K.Pidathala, C.Berry, N.Biangini, G.A.Leung, S.C.Hasnain, S.S.Antonyuk, S.V.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial444Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial420Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b378Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial239Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial196Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 799Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 875Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrial64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial46Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 959Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BA [auth E],
DA [auth G],
M [auth A],
R [auth C],
W [auth D]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE
Query on PEE

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AA [auth E],
S [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
PX4
Query on PX4

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Y [auth E]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
HEC
Query on HEC

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U [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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N [auth C],
O [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

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P [auth C]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
6PE
Query on 6PE

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K [auth A]1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
JGW (Subject of Investigation/LOI)
Query on JGW

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T [auth C]2-methyl-3-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]-3~{H}-quinolin-4-one
C24 H18 F3 N O2
GICIDYUDUAQJFR-QFIPXVFZSA-N
PG4
Query on PG4

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Q [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES
Query on FES

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X [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4
Query on PO4

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CA [auth F]
EA [auth G]
FA [auth G]
GA [auth G]
L [auth A]
CA [auth F],
EA [auth G],
FA [auth G],
GA [auth G],
L [auth A],
V [auth D],
Z [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.56α = 90
b = 209.56β = 90
c = 343.348γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 2.0: 2024-01-24
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary