3I9V Oxidoreductase date Jul 13, 2009
title Crystal Structure Of The Hydrophilic Domain Of Respiratory C From Thermus Thermophilus, Oxidized, 2 Molasu
authors L.A.Sazanov, J.M.Berrisford
compound source
Molecule: Nadh-Quinone Oxidoreductase Subunit 1
Chain: 1, A
Synonym: Nadh Dehydrogenase I Chain 1, Ndh-1 Subunit 1
Ec: 1.6.99.5
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 2
Chain: 2, B
Synonym: Nadh Dehydrogenase I Chain 2, Ndh-1 Subunit 2
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 3
Chain: 3, C
Synonym: Nadh Dehydrogenase I Chain 3, Ndh-1 Subunit 3
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 4
Chain: 4, D
Synonym: Nadh Dehydrogenase I Chain 4, Ndh-1 Subunit 4
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 5
Chain: 5, E
Synonym: Nadh Dehydrogenase I Chain 5, Ndh-1 Subunit 5
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 6
Chain: 6, F
Synonym: Nadh Dehydrogenase I Subunit 6, Ndh-1 Subunit 6
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 9
Chain: 9, G
Synonym: Nadh Dehydrogenase I Subunit 9, Ndh-1 Subunit 9
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579

Molecule: Nadh-Quinone Oxidoreductase Subunit 15
Chain: 7, H
Synonym: Nadh Dehydrogenase I Chain 15, Ndh-1 Subunit 15
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634 Dsm 579
symmetry Space Group: P 1 21 1
R_factor 0.235 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.963 150.514 216.726 90.00 92.19 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand CA, FES, FMN, MN, SF4 enzyme Oxidoreductase E.C.1.6.99.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
3, C


4, D


7, H


9, G


A, 1


B, 2


E, 5


F, 6


Primary referenceStructural basis for the mechanism of respiratory complex I., Berrisford JM, Sazanov LA, J Biol Chem. 2009 Jul 27. PMID:19635800
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (759 Kb) [Save to disk]
  • Biological Unit Coordinates (3i9v.pdb1.gz) 378 Kb
  • Biological Unit Coordinates (3i9v.pdb2.gz) 382 Kb
  • LPC: Ligand-Protein Contacts for 3I9V
  • CSU: Contacts of Structural Units for 3I9V
  • Structure Factors (969 Kb)
  • Retrieve 3I9V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I9V from S2C, [Save to disk]
  • Re-refined 3i9v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3I9V 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 3I9V
  • 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 3I9V, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i9v_3] [3i9v] [3i9v_4] [3i9v_G] [3i9v_6] [3i9v_E] [3i9v_A] [3i9v_9] [3i9v_5] [3i9v_C] [3i9v_D] [3i9v_7] [3i9v_2] [3i9v_B] [3i9v_1] [3i9v_F] [3i9v_H]
  • SWISS-PROT database: [Q5SKZ7] [Q56222] [Q56221] [Q56223] [Q56220] [Q56219] [Q56218] [Q56224]
  • Belongs to the h(+) or na(+)-translocating nadh dehydrogenase (ndh) family according to TCDB.
  • Domain organization of [NQO15_THET8] [NQO1_THET8] [NQO2_THET8] [NQO3_THET8] [NQO4_THET8] [NQO5_THET8] [NQO6_THET8] [NQO9_THET8] by SWISSPFAM
  • Domains found in 3I9V: [Molybdop_Fe4S4] [NADH-G_4Fe-4S_3] [NADH_4Fe-4S ] by SMART
    • Other resources with information on 3I9V
  • Community annotation for 3I9V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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