5JWA Membrane Protein Inhibitor date May 11, 2016
title The Structure Of Malaria Pfndh2
authors Y.Yu, Y.Q.Yang, X.L.Li, J.Yu, J.P.Ge, J.Li, Y.Rao, M.J.Yang
compound source
Molecule: Nadh Dehydrogenase, Putative
Chain: A, H
Fragment: Unp Residues 25-533
Ec: 1.6.99.3
Engineered: Yes
 Organism_scientific: Plasmodium Falciparum (Isolate 3d7)
Organism_taxid: 36329
Strain: Isolate 3d7
Gene: Pfi0735c
Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4;
Expression_system_taxid: 1182032
symmetry Space Group: I 41
R_factor 0.188 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
191.670 191.670 91.388 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.16 Å
ligand ACT, FAD, MG, TRT enzyme Oxidoreductase E.C.1.6.99.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H, A


Primary referenceTarget Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria., Yang Y, Yu Y, Li X, Li J, Wu Y, Yu J, Ge J, Huang Z, Jiang L, Rao Y, Yang M, J Med Chem. 2017 Mar 9;60(5):1994-2005. doi: 10.1021/acs.jmedchem.6b01733. Epub, 2017 Feb 22. PMID:28195463
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (180 Kb) [Save to disk]
  • Biological Unit Coordinates (5jwa.pdb1.gz) 173 Kb
  • LPC: Ligand-Protein Contacts for 5JWA
  • CSU: Contacts of Structural Units for 5JWA
  • Structure Factors (2022 Kb)
  • Retrieve 5JWA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JWA from S2C, [Save to disk]
  • Re-refined 5jwa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JWA 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 5JWA
  • 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: [5jwa_H] [5jwa] [5jwa_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JWA
  • Community annotation for 5JWA at PDBWiki (http://pdbwiki.org)

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