4NFW Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli date
authors Hong, M.K., Kim, J.K., Kang, L.W.
compound source
symmetry
R_factor
R_Free 0.28900
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.30
ligand MN, SO4 enzyme
Gene I14
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Primary referenceDivalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli., Hong MK, Ribeiro AJ, Kim JK, Ngo HP, Kim J, Lee CH, Ahn YJ, Fernandes PA, Li Q, Ramos MJ, Kang LW, Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1297-310. doi:, 10.1107/S1399004714002570. Epub 2014 Apr 29. PMID:24816099
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (312 Kb) [Save to disk]
  • Biological Unit Coordinates (4nfw.pdb1.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb2.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb3.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb4.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb5.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb6.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb7.gz) 31 Kb
  • Biological Unit Coordinates (4nfw.pdb8.gz) 30 Kb
  • Biological Unit Coordinates (4nfw.pdb9.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 4NFW
  • CSU: Contacts of Structural Units for 4NFW
  • Structure Factors (2544 Kb)
  • Retrieve 4NFW in mmCIF format [Save to disk]
  • Re-refined 4nfw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4NFW 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 4NFW
  • 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 4NFW, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nfw_A] [4nfw_D] [4nfw] [4nfw_F] [4nfw_K] [4nfw_H] [4nfw_L] [4nfw_B] [4nfw_C] [4nfw_I] [4nfw_J] [4nfw_G] [4nfw_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4NFW
  • Community annotation for 4NFW at PDBWiki (http://pdbwiki.org)

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