2C7M Protein Binding date Nov 25, 2005
title Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
authors L.Penengo, M.Mapelli, A.G.Murachelli, S.Confalioneri, L.Magri, A.Musacchio, P.P.Di Fiore, S.Polo, T.R.Schneider
compound source
Molecule: Rab Guanine Nucleotide Exchange Factor 1
Chain: A
Fragment: Two Ubiqutin Binding Domains, Residues 1-74
Synonym: Rabex-5, Gef 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: B

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Other_details: Boston Biochem
symmetry Space Group: P 61
R_factor 0.183 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.900 81.900 55.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin., Penengo L, Mapelli M, Murachelli AG, Confalonieri S, Magri L, Musacchio A, Di Fiore PP, Polo S, Schneider TR, Cell. 2006 Mar 24;124(6):1183-95. Epub 2006 Feb 23. PMID:16499958
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (2c7m.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 2C7M
  • CSU: Contacts of Structural Units for 2C7M
  • Likely Quarternary Molecular Structure file(s) for 2C7M
  • Structure Factors (53 Kb)
  • Retrieve 2C7M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C7M from S2C, [Save to disk]
  • Re-refined 2c7m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C7M 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 2C7M
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2C7M, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c7m_A] [2c7m_B] [2c7m]
  • SWISS-PROT database: [Q9UJ41] [P62990]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [RABX5_HUMAN] [UBIQ_BOVIN] by SWISSPFAM
  • Domains found in 2C7M: [UBQ] [ZnF_A20 ] by SMART
  • Other resources with information on 2C7M
  • Community annotation for 2C7M 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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