2VUK Transcription date May 26, 2008
title Structure Of The P53 Core Domain Mutant Y220c Bound To The Stabilizing Small-Molecule Drug Phikan083
authors A.C.Joerger, F.M.Boeckler, A.R.Fersht
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B
Fragment: Dna-Binding Domain, Residues 94-312
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13, P53;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.093 71.234 105.207 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.5 Å
ligand P83, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceTargeted rescue of a destabilized mutant of p53 by an in silico screened drug., Boeckler FM, Joerger AC, Jaggi G, Rutherford TJ, Veprintsev DB, Fersht AR, Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10360-5. Epub 2008 Jul 23. PMID:18650397
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2vuk.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (2vuk.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2VUK
  • CSU: Contacts of Structural Units for 2VUK
  • Likely Quarternary Molecular Structure file(s) for 2VUK
  • Structure Factors (544 Kb)
  • Retrieve 2VUK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VUK from S2C, [Save to disk]
  • Re-refined 2vuk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VUK 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 2VUK
  • 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 2VUK, from MSDmotif at EBI
  • Fold representative 2vuk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vuk_A] [2vuk] [2vuk_B]
  • SWISS-PROT database: [P04637]
  • Belongs to the pore-forming pnc-27 peptide of 32 aas from the p53 tumor suppressor protein (pnc-27) family according to TCDB.
  • Domain organization of [P53_HUMAN] by SWISSPFAM
  • Other resources with information on 2VUK
  • Community annotation for 2VUK 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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