2WDV

E. coli succinate:quinone oxidoreductase (SQR) with an empty quinone- binding pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 2WDV

Classification: OXIDOREDUCTASE

Total Structure Weight: 362614.72

Macromolecule Entities
Molecule Chains Length Organism Details
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT A, E, I 588 Escherichia coli EC#: 1.3.5.1 IUBMB
Details: FAD ATOM C8M IS COVALENTLY LINKED TO NE2 OF SDHA HIS45
Gene Name(s): sdhA b0723 JW0713
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT B, F, J 238 Escherichia coli EC#: 1.3.5.1 IUBMB
Gene Name(s): sdhB b0724 JW0714
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT C, G, K 129 Escherichia coli EC#: 1.3.5.1 IUBMB
Details: RESIDUES 8-128 MODELLED
Gene Name(s): sdhC cybA b0721 JW0711
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN D, H, L 115 Escherichia coli EC#: 1.3.5.1 IUBMB
Details: RESIDUES 11-115 MODELLED
Gene Name(s): sdhD b0722 JW0712
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex II

Protein Name: Succinate:quinone oxidoreductase (SQR, Complex II)


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, E, I FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C, G, K PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

B, F, J IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

B, F, J FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

B, F, J FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TEO
Query on TEO

A, E, I MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, E, I SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.205
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 120.34 α = 90.00
b = 184.85 β = 90.00
c = 204.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-26
  • Released Date: 2009-08-25
  • Deposition author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Revision History

  • Version 1_0: 2009-08-25

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance