3RKO Oxidoreductase date Apr 18, 2011
title Crystal Structure Of The Membrane Domain Of Respiratory Comp E. Coli At 3.0 Angstrom Resolution
authors R.G.Efremov, L.A.Sazanov
compound source
Molecule: Nadh-Quinone Oxidoreductase Subunit L
Chain: L, B
Synonym: Proton-Translocating Nadh-Quinone Oxidoreductase,
Ec: 1.6.5.3
Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit M
Chain: M, C
Synonym: Proton-Translocating Nadh-Quinone Oxidoreductase,
Ec: 1.6.5.3

Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit N
Chain: N, D
Synonym: Nadh Dehydrogenase I Subunit N 1, Ndh-1 Subunit N
Ec: 1.6.5.3

Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit K
Chain: K, G
Synonym: Nadh Dehydrogenase I Subunit K, Ndh-1 Subunit K
Ec: 1.6.5.3

Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit A
Chain: A, E
Ec: 1.6.5.3

Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane

Molecule: Nadh-Quinone Oxidoreductase Subunit J
Chain: J, F
Synonym: Nadh Dehydrogenase Subunit J
Ec: 1.6.5.3

Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
Other_details: Cytoplasmic Membrane
symmetry Space Group: P 1
R_factor 0.232 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.980 116.570 191.370 98.51 104.08 108.51
method X-Ray Diffractionresolution 3.00 Å
ligand CA7, LFA enzyme Oxidoreductase E.C.1.6.5.3 BRENDA
note 3RKO (Molecule of the Month:pdb144)
Gene
Ontology
ChainFunctionProcessComponent
A, E


B, L


F, J


K, G


M, C


N, D


Primary referenceStructure of the membrane domain of respiratory complex I., Efremov RG, Sazanov LA, Nature. 2011 Aug 7. doi: 10.1038/nature10330. PMID:21822288
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1262 Kb) [Save to disk]
  • Biological Unit Coordinates (3rko.pdb1.gz) 627 Kb
  • Biological Unit Coordinates (3rko.pdb2.gz) 628 Kb
  • LPC: Ligand-Protein Contacts for 3RKO
  • CSU: Contacts of Structural Units for 3RKO
  • Structure Factors (1047 Kb)
  • Retrieve 3RKO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RKO from S2C, [Save to disk]
  • Re-refined 3rko structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RKO in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3RKO
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3RKO, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rko_A] [3rko_L] [3rko_G] [3rko_F] [3rko_B] [3rko_K] [3rko_D] [3rko_N] [3rko_C] [3rko_E] [3rko] [3rko_J] [3rko_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RKO
  • Community annotation for 3RKO at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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