5NA4 Oxidoreductase date Feb 27, 2017
title Nadh:Quinone Oxidoreductase (Ndh-II) From Staphylococcus Aur E172s Mutant
authors J.A.Brito, D.Athayde, F.M.Sousa, F.V.Sena, M.M.Pereira, M.Archer
compound source
Molecule: Nadh Dehydrogenase-Like Protein Saouhsc_00878
Chain: A
Ec: 1.6.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Saouhsc_00878
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 3 2
R_factor 0.175 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
151.275 151.275 151.275 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand FAD enzyme Oxidoreductase E.C.1.6.99 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus., Sousa FM, Sena FV, Batista AP, Athayde D, Brito JA, Archer M, Oliveira ASF, Soares CM, Catarino T, Pereira MM, Biochim Biophys Acta. 2017 Oct;1858(10):823-832. doi:, 10.1016/j.bbabio.2017.08.002. Epub 2017 Aug 8. PMID:28801048
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (5na4.pdb1.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 5NA4
  • CSU: Contacts of Structural Units for 5NA4
  • Structure Factors (862 Kb)
  • Retrieve 5NA4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NA4 from S2C, [Save to disk]
  • View 5NA4 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 5NA4
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5na4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NA4
  • Community annotation for 5NA4 at PDBWiki (http://pdbwiki.org)

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