4MDT Structure of LpxC bound to the reaction product UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine date 2013-08-23
authors Clayton, G.M., Klein, D.J., Rickert, K.W., Patel, S.B., Kornienko, M., Zugay-Murphy, J., Reid, J.C., Tummala, S., Sharma, S., Singh, S.B., Miesel, L., Lumb, K.J., Soisson, S.M.
compound source
symmetry
R_factor
R_Free 0.2402
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.59
ligand 24G, PO4, ZN enzyme
Gene O3O
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer., Clayton GM, Klein DJ, Rickert KW, Patel SB, Kornienko M, Zugay-Murphy J, Reid JC, Tummala S, Sharma S, Singh SB, Miesel L, Lumb KJ, Soisson SM, J Biol Chem. 2013 Oct 9. PMID:24108127
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (4mdt.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (4mdt.pdb2.gz) 54 Kb
  • Biological Unit Coordinates (4mdt.pdb3.gz) 54 Kb
  • Biological Unit Coordinates (4mdt.pdb4.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 4MDT
  • CSU: Contacts of Structural Units for 4MDT
  • Structure Factors (404 Kb)
  • Retrieve 4MDT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MDT from S2C, [Save to disk]
  • Re-refined 4mdt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4MDT 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 4MDT
  • 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 4MDT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4mdt_C] [4mdt_B] [4mdt] [4mdt_D] [4mdt_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4MDT
  • Community annotation for 4MDT at PDBWiki (http://pdbwiki.org)

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