2GF9 Protein Transport date Mar 21, 2006
title Crystal Structure Of Human Rab3d In Complex With Gdp
authors B.Hong, J.Wang, L.Shen, W.Tempel, R.Landry, C.H.Arrowsmith, A.M.Ed M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomic Consortium (Sgc)
compound source
Molecule: Ras-Related Protein Rab-3d
Chain: A
Fragment: Residues 20-189
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab3d, Gov, Rab16
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De-3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P28a-Lic
symmetry Space Group: P 21 21 21
R_factor 0.153 R_Free 0.185
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.700 63.222 67.695 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.53 Å
ligand GDP, MG, UNX enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (2gf9.pdb1.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 2GF9
  • CSU: Contacts of Structural Units for 2GF9
  • Likely Quarternary Molecular Structure file(s) for 2GF9
  • Structure Factors (411 Kb)
  • Retrieve 2GF9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GF9 from S2C, [Save to disk]
  • Re-refined 2gf9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2GF9 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 2GF9
  • 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 2GF9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gf9_A] [2gf9]
  • SWISS-PROT database: [O95716]
  • Domain organization of [RAB3D_HUMAN] by SWISSPFAM
  • Domain found in 2GF9: [RAB ] by SMART
    • Other resources with information on 2GF9
  • Community annotation for 2GF9 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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