3VBG Ligase Ligase Activator date Jan 02, 2012
title Structure Of Hdm2 With Dimer Inducing Indolyl Hydantoin Ro-2
authors C.M.Lukacs, C.A.Janson, B.J.Graves
compound source
Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: A, B, C, D
Fragment: Unp Residues 25-109
Synonym: Double Minute 2 Protein, Hdm2, Oncoprotein Mdm2, P Protein Mdm2;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Human
Gene: Mdm2
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe40
symmetry Space Group: P 32
R_factor 0.182 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.392 64.392 167.587 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand 03M enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceActivation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization., Graves B, Thompson T, Xia M, Janson C, Lukacs C, Deo D, Di Lello P, Fry D, Garvie C, Huang KS, Gao L, Tovar C, Lovey A, Wanner J, Vassilev LT, Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11788-93. Epub 2012 Jun 28. PMID:22745160
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (3vbg.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3vbg.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 3VBG
  • CSU: Contacts of Structural Units for 3VBG
  • Structure Factors (290 Kb)
  • Retrieve 3VBG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VBG from S2C, [Save to disk]
  • Re-refined 3vbg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VBG 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 3VBG
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3VBG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vbg_C] [3vbg_B] [3vbg_A] [3vbg_D] [3vbg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VBG
  • Community annotation for 3VBG at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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