2ACZ

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.308
  • R-Value Work: 0.264

Literature

Macromolecules
Sequence Display for 2ACZ

Classification: Oxidoreductase / Electron transport

Total Structure Weight: 122367.34

Macromolecule Entities
Molecule Chains Length Organism Details
Succinate dehydrogenase flavoprotein subunit A 588 Escherichia coli EC#: 1.3.5.1 IUBMB
Gene Name(s): sdhA b0723 JW0713
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Succinate dehydrogenase iron-sulfur protein B 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 129 Escherichia coli Gene Name(s): sdhC cybA b0721 JW0711
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Succinate dehydrogenase hydrophobic membrane anchor protein D 115 Escherichia coli 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 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDN
Query on CDN

C CARDIOLIPIN
C58 H120 O17 P2
GKRASOJOCMJQMF-DUXRJKJQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FAD
Query on FAD

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

C HEME B/C
HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE) (Synonym)
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AT5
Query on AT5

C 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1- OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE
ATPENIN A5; AA5 (Synonym)
C15 H21 Cl2 N O5
OVULNOOPECCZRG-CIUDSAMLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

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

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

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

A OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.308
  • R-Value Work: 0.264
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 138.76 α = 90.00
b = 138.76 β = 90.00
c = 521.87 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-07-19
  • Released Date: 2006-01-03
  • Deposition author(s): Horsefield, R., Yankovskaya, V., Sexton, G., Whittingham, W., Shiomi, K., Omura, S., Byrne, B., Cecchini, G., Iwata, S.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance