3L0I Protein Binding Protein Transport date Dec 10, 2009
title Complex Structure Of Sidmdrra With The Wild Type Rab1
authors Y.Zhu, F.Shao
compound source
Molecule: Drra
Chain: A, C
Fragment: Gefgdf Domain, Residues 193-550
Synonym: Sidm
Engineered: Yes
Organism_scientific: Legionella Pneumophila
Organism_taxid: 446
Gene: Sidm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-2

Molecule: Ras-Related Protein Rab-1a
Chain: B, D
Fragment: Small Gtpase Domain, Residues 1-177
Synonym: Ypt1-Related Protein, Rab1a
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1a
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
63.808 71.747 146.911 90.00 93.62 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand CL, MSE, SO4 enzyme
A, C

D, B

Primary referenceStructural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA., Zhu Y, Hu L, Zhou Y, Yao Q, Liu L, Shao F, Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4699-704. Epub 2010 Feb 22. PMID:20176951
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (3l0i.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (3l0i.pdb2.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 3L0I
  • CSU: Contacts of Structural Units for 3L0I
  • Structure Factors (1430 Kb)
  • Retrieve 3L0I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L0I from S2C, [Save to disk]
  • Re-refined 3l0i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L0I 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 3L0I
  • 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 3L0I, from MSDmotif at EBI
  • Fold representative 3l0i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l0i_C] [3l0i] [3l0i_B] [3l0i_D] [3l0i_A]
  • SWISS-PROT database: [Q29ST3] [P62820]
  • Domain organization of [Q29ST3_LEGPN] [RAB1A_HUMAN] by SWISSPFAM
  • Domain found in 3L0I: [RAB ] by SMART
  • Other resources with information on 3L0I
  • Community annotation for 3L0I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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