1NEK

Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound

Structural Biology Knowledgebase: 1NEK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NEK

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT

Total Structure Weight: 123108.48

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
Succinate dehydrogenase iron-sulfur protein B 238 Escherichia coli EC#: 1.3.5.1 IUBMB
Gene Name(s): sdhB b0724 JW0714
Succinate dehydrogenase cytochrome b-556 subunit C 129 Escherichia coli Gene Name(s): sdhC cybA b0721 JW0711
Succinate dehydrogenase hydrophobic membrane anchor protein D 115 Escherichia coli Gene Name(s): sdhD b0722 JW0712

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 10 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FAD
Query on FAD

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

C L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL- PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

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

B IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UQ2
Query on UQ2

D UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

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

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

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

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.247
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 138.80 α = 90.00
b = 138.80 β = 90.00
c = 521.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-11
  • Released Date: 2003-02-25
  • Deposition author(s): Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4