1TXU Protein Transport date Jul 06, 2004
title Crystal Structure Of The Vps9 Domain Of Rabex-5
authors A.Delprato, E.Merithew, D.G.Lambright
compound source
Molecule: Rab5 Gdpgtp Exchange Factor
Chain: A
Fragment: Vps9
Synonym: Rabex-5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Rabgef1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 2
R_factor 0.227 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.047 88.329 47.299 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand MG, MSE enzyme
note 1TXU is a representative structure
Primary referenceStructure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5., Delprato A, Merithew E, Lambright DG, Cell 2004 Sep 3;118(5):607-17. PMID:15339665
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1txu.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1TXU
  • CSU: Contacts of Structural Units for 1TXU
  • Likely Quarternary Molecular Structure file(s) for 1TXU
  • Retrieve 1TXU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TXU from S2C, [Save to disk]
  • View 1TXU 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 1TXU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1TXU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1txua_, region A [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1txu_A] [1txu]
  • SWISS-PROT database: [Q9UJ41]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [RABX5_HUMAN] by SWISSPFAM
  • Domain found in 1TXU: [VPS9 ] by SMART
  • Other resources with information on 1TXU
  • Community annotation for 1TXU 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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