4KYI Protein Binding Transport Protein date May 29, 2013
title Crystal Structure Of The Phospholipase Vipd From Legionella Pneumophila In Complex With The Human Gtpase Rab5
authors M.Lucas, A.H.Gaspar, C.Pallara, A.L.Rojas, J.Fernandez-Recio, M.P A.Hierro
compound source
Molecule: Vipd
Chain: A, C, E, G
Fragment: Unp Residues 19-564
Engineered: Yes
Organism_scientific: Legionella Pneumophila Subsp. Pneumoph
Organism_taxid: 272624
Strain: Philadelphia 1 Atcc 33152 Dsm 7513
Gene: Vipd, Lpg2831
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ras-Related Protein Rab-5c
Chain: B, D, F, H
Fragment: Unp Residues 18-182
Synonym: L1880, Rab5l
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab5c, Rabl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.233 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
94.275 97.976 109.849 76.57 80.71 78.91
method X-Ray Diffractionresolution 3.08 Å
ligand EDO, GNP, GOL, MG enzyme
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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KYI, from MSDmotif at EBI
  • Fold representative 4kyi from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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