4KYI Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5 date
authors Lucas, M., Gaspar, A.H., Pallara, C., Rojas, A.L., Fernandez-Recio, J., Machner, M.P., Hierro, A.
compound source
symmetry
R_factor
R_Free 0.2803
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.08
ligand EDO, GNP, GOL, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceStructural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5., Lucas M, Gaspar AH, Pallara C, Rojas AL, Fernandez-Recio J, Machner MP, Hierro A, Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):E3514-23. doi:, 10.1073/pnas.1405391111. Epub 2014 Aug 11. PMID:25114243
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (403 Kb) [Save to disk]
  • Biological Unit Coordinates (4kyi.pdb1.gz) 105 Kb
  • Biological Unit Coordinates (4kyi.pdb2.gz) 104 Kb
  • Biological Unit Coordinates (4kyi.pdb3.gz) 104 Kb
  • Biological Unit Coordinates (4kyi.pdb4.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 4KYI
  • CSU: Contacts of Structural Units for 4KYI
  • Structure Factors (371 Kb)
  • Retrieve 4KYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KYI from S2C, [Save to disk]
  • Re-refined 4kyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KYI 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 4KYI
  • 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 4KYI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kyi_G] [4kyi] [4kyi_H] [4kyi_B] [4kyi_D] [4kyi_C] [4kyi_E] [4kyi_F] [4kyi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KYI: [RAB ] by SMART
  • Other resources with information on 4KYI
  • Community annotation for 4KYI at PDBWiki (http://pdbwiki.org)

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