2D3G Protein Transport date Sep 28, 2005
title Double Sided Ubiquitin Binding Of Hrs-Uim
authors S.Hirano, M.Kawasaki, R.Kato, S.Wakatsuki
compound source
Molecule: Ubiquitin
Chain: A, B
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquitin Interacting Motif From Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate;
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Human Hrs And Was Synthesized By Standard Peptide Synthesis Methods.
symmetry Space Group: H 3 2
R_factor 0.197 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.244 73.244 169.636 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
Primary referenceDouble-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting., Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, Stenmark H, Wakatsuki S, Nat Struct Mol Biol. 2006 Mar;13(3):272-7. Epub 2006 Feb 5. PMID:16462748
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (2d3g.pdb1.gz) 29 Kb
  • CSU: Contacts of Structural Units for 2D3G
  • Likely Quarternary Molecular Structure file(s) for 2D3G
  • Structure Factors (145 Kb)
  • Retrieve 2D3G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D3G from S2C, [Save to disk]
  • Re-refined 2d3g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D3G 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 2D3G
  • 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 2D3G, from MSDmotif at EBI
  • Fold representative 2d3g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d3g_B] [2d3g_A] [2d3g] [2d3g_P]
  • SWISS-PROT database: [O14964] [P62990]
  • Domain organization of [HGS_HUMAN] [UBIQ_BOVIN] by SWISSPFAM
  • Domains found in 2D3G: [UBQ] [UIM ] by SMART
  • Other resources with information on 2D3G
  • Community annotation for 2D3G 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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