2WDQ

E. coli succinate:quinone oxidoreductase (SQR) with carboxin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.

Ruprecht, J.Yankovskaya, V.Maklashina, E.Iwata, S.Cecchini, G.

(2009) J Biol Chem 284: 29836-29846

  • DOI: 10.1074/jbc.M109.010058
  • Primary Citation of Related Structures:  
    2WDQ, 2WDR, 2WDV

  • PubMed Abstract: 
  • Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site ...

    Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.


    Organizational Affiliation

    Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW72AZ, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNITA, E, I588Escherichia coliMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12))
Explore P0AC41 
Go to UniProtKB:  P0AC41
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNITB, F, J238Escherichia coliMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P07014 (Escherichia coli (strain K12))
Explore P07014 
Go to UniProtKB:  P07014
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNITC, G, K129Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P69054 (Escherichia coli (strain K12))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNITD, H, L115Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12))
Explore P0AC44 
Go to UniProtKB:  P0AC44
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
EA [auth I], M [auth A], V [auth E]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
CA [auth G], LA [auth K], T [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth F], JA [auth J], R [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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BA [auth F], KA [auth J], S [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
CBE (Subject of Investigation/LOI)
Query on CBE

Download Ideal Coordinates CCD File 
DA [auth G], MA [auth K], U [auth C]2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
IA [auth J], Q [auth B], Z [auth F]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TEO
Query on TEO

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FA [auth I], N [auth A], W [auth E]MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
HA [auth I], P [auth A], Y [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth I], O [auth A], X [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.4α = 90
b = 178.46β = 90
c = 200.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references, Experimental preparation