1Z0D Protein Transport date Mar 01, 2005
title Gdp-Bound Rab5c Gtpase
authors S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright
compound source
Molecule: Ras-Related Protein Rab-5c
Chain: A, C
Fragment: Gtpase Domain
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Rab5c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Codon Plus-Ril Cells
Expression_system_vector_type: Gst Fusion, Pgex
Expression_system_plasmid: Pgex4t1
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.401 70.931 137.610 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand GDP, MG, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural basis of family-wide Rab GTPase recognition by rabenosyn-5., Eathiraj S, Pan X, Ritacco C, Lambright DG, Nature 2005 Jul 21;436(7049):415-9. PMID:16034420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1z0d.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (1z0d.pdb2.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 1Z0D
  • CSU: Contacts of Structural Units for 1Z0D
  • Likely Quarternary Molecular Structure file(s) for 1Z0D
  • Structure Factors (223 Kb)
  • Retrieve 1Z0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Z0D from S2C, [Save to disk]
  • Re-refined 1z0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Z0D 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 1Z0D
  • 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 1Z0D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1z0d_A] [1z0d_C] [1z0d]
  • SWISS-PROT database: [P35278]
  • Domain organization of [RAB5C_MOUSE] by SWISSPFAM
  • Domain found in 1Z0D: [RAB ] by SMART
  • Other resources with information on 1Z0D
  • Community annotation for 1Z0D 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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