3M9S Oxidoreductase date Mar 22, 2010
title Crystal Structure Of Respiratory Complex I From Thermus Ther
authors R.G.Efremov, R.Baradaran, L.A.Sazanov
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

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

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

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

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

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

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

Molecule: Nadh-Quinone Oxidoreductase Subunit 15
Chain: 7, J
Synonym: Nadh Dehydrogenase I Chain 15, Ndh-1 Subunit 15
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Nadh-Quinone Oxidoreductase Subunit 12
Chain: L, O
Synonym: Nadh Dehydrogenase I Chain 12, Ndh-1 Subunit 12
Ec: 1.6.99.5
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Nadh-Quinone Oxidoreductase Subunit 13
Chain: M, P
Ec: 1.6.5.3
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Nadh-Quinone Oxidoreductase Subunit 14
Chain: N, Q
Ec: 1.6.5.3
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Nadh-Quinone Oxidoreductase Subunits 7, 10 And 11
Chain: R, S
Ec: 1.6.5.3
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Nadh-Quinone Oxidoreductase Subunit 8
Chain: H, T
Ec: 1.6.5.3
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 1 21 1
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.390 336.090 262.240 90.00 100.59 90.00
method X-Ray Diffractionresolution 4.50 Å
ligand FES, FMN, SF4 enzyme Oxidoreductase E.C.1.6.99.5 BRENDA
note 3M9S (Molecule of the Month:pdb144)
Gene
Ontology
ChainFunctionProcessComponent
3, C


4, D


9, G


A, 1


B, 2


E, 5


F, 6


J, 7


Primary referenceThe architecture of respiratory complex I., Efremov RG, Baradaran R, Sazanov LA, Nature. 2010 May 27;465(7297):441-5. PMID:20505720
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (810 Kb) [Save to disk]
  • Biological Unit Coordinates (3m9s.pdb1.gz) 405 Kb
  • Biological Unit Coordinates (3m9s.pdb2.gz) 405 Kb
  • LPC: Ligand-Protein Contacts for 3M9S
  • CSU: Contacts of Structural Units for 3M9S
  • Structure Factors (3553 Kb)
  • Retrieve 3M9S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M9S from S2C, [Save to disk]
    • View 3M9S 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 3M9S
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3M9S, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m9s_N] [3m9s_J] [3m9s_T] [3m9s_D] [3m9s_L] [3m9s_R] [3m9s_9] [3m9s_M] [3m9s_5] [3m9s_H] [3m9s_2] [3m9s_O] [3m9s_Q] [3m9s_6] [3m9s_F] [3m9s_4] [3m9s_B] [3m9s_7] [3m9s] [3m9s_C] [3m9s_E] [3m9s_P] [3m9s_3] [3m9s_1] [3m9s_A] [3m9s_S] [3m9s_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3M9S: [Molybdop_Fe4S4] [NADH-G_4Fe-4S_3] [NADH_4Fe-4S ] by SMART
    • Other resources with information on 3M9S
  • Community annotation for 3M9S 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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