3DZ8 Protein Transport date Jul 29, 2008
title Crystal Structure Of Human Rab3b Gtpase Bound With Gdp
authors Y.Shen, Y.Tong, D.Sukumar, W.Tempel, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, M.Wilkstrom, A.Bochkarev, H.Park, Struct Genomics Consortium (Sgc)
compound source
Molecule: Ras-Related Protein Rab-3b
Chain: A
Fragment: Unp Residues 18-190
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab3b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-V2r
Expression_system_plasmid: Pet28-Mhl (Gi:134105571)
symmetry Space Group: C 1 2 1
R_factor 0.211 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.969 50.875 73.553 90.00 110.91 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GDP, UNX enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (3dz8.pdb1.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3DZ8
  • CSU: Contacts of Structural Units for 3DZ8
  • Likely Quarternary Molecular Structure file(s) for 3DZ8
  • Structure Factors (227 Kb)
  • Retrieve 3DZ8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DZ8 from S2C, [Save to disk]
  • Re-refined 3dz8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DZ8 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 3DZ8
  • 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 3DZ8, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dz8] [3dz8_A]
  • SWISS-PROT database: [P20337]
  • Domain organization of [RAB3B_HUMAN] by SWISSPFAM
  • Domain found in 3DZ8: [RAB ] by SMART
    • Other resources with information on 3DZ8
  • Community annotation for 3DZ8 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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