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
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
  • Alignments of the sequence of 2YBG with the sequences similar proteins can be viewed for 2YBG's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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