3BUM Ligase date Jan 03, 2008
title Crystal Structure Of C-Cbl-Tkb Domain Complexed With Its Bin In Sprouty2
authors C.Ng, A.R.Jackson, P.J.Buschdorf, Q.Sun, R.G.Guy, J.Sivaraman
compound source
Molecule: Protein Sprouty Homolog 2
Chain: A
Fragment: Unp Residues 49-61
Synonym: Spry-2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Spry2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t1

Molecule: E3 Ubiquitin-Protein Ligase Cbl
Chain: B
Fragment: C-Cbl Tkb Domain, Unp Residues 25-351
Synonym: Signal Transduction Protein Cbl, Proto-Oncogene C- Casitas B-Lineage Lymphoma Proto-Oncogene, Ring Finger Prot
Ec: 6.3.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cbl, Cbl2, Rnf55
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t1
symmetry Space Group: P 6
R_factor 0.224 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.256 122.256 54.707 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand PTR enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates., Ng C, Jackson RA, Buschdorf JP, Sun Q, Guy GR, Sivaraman J, EMBO J. 2008 Feb 14;. PMID:18273061
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (3bum.pdb1.gz) 3 Kb
  • Biological Unit Coordinates (3bum.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (3bum.pdb3.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 3BUM
  • CSU: Contacts of Structural Units for 3BUM
  • Likely Quarternary Molecular Structure file(s) for 3BUM
  • Structure Factors (357 Kb)
  • Retrieve 3BUM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BUM from S2C, [Save to disk]
  • Re-refined 3bum structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BUM 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 3BUM
  • 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 3BUM, from MSDmotif at EBI
  • Fold representative 3bum from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bum_B] [3bum] [3bum_A]
  • SWISS-PROT database: [P22681] [O43597]
  • Domain organization of [CBL_HUMAN] [SPY2_HUMAN] by SWISSPFAM
  • Other resources with information on 3BUM
  • Community annotation for 3BUM 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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