2YBG Cell Cycle date Mar 08, 2011
title Structure Of Lys120-Acetylated P53 Core Domain
authors E.Arbely, M.D.Allen, A.C.Joerger, A.R.Fersht
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B, C, D
Fragment: Dna-Binding Domain, Residues 94-293
Synonym: Antigen Ny-Co-13, Phosphoprotein P53, Tumor Suppre P53, P53;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.1744 R_Free 0.2260
length a length b length c angle alpha angle beta angle gamma
68.926 69.581 83.494 90.00 90.12 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ALY, ZN enzyme
A, D, C, B

Primary referenceAcetylation of lysine 120 of p53 endows DNA-binding specificity at effective physiological salt concentration., Arbely E, Natan E, Brandt T, Allen MD, Veprintsev DB, Robinson CV, Chin JW, Joerger AC, Fersht AR, Proc Natl Acad Sci U S A. 2011 May 17;108(20):8251-6. Epub 2011 Apr 27. PMID:21525412
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (2ybg.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (2ybg.pdb2.gz) 36 Kb
  • Biological Unit Coordinates (2ybg.pdb3.gz) 36 Kb
  • Biological Unit Coordinates (2ybg.pdb4.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 2YBG
  • CSU: Contacts of Structural Units for 2YBG
  • Structure Factors (2801 Kb)
  • Retrieve 2YBG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YBG from S2C, [Save to disk]
  • Re-refined 2ybg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YBG 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 2YBG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2YBG, from MSDmotif at EBI
  • Fold representative 2ybg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ybg_C] [2ybg_B] [2ybg] [2ybg_D] [2ybg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YBG
  • Community annotation for 2YBG 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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