4AGM Cell Cycle date Jan 30, 2012
title Structure Of The P53 Core Domain Mutant Y220c Bound To The Stabilizing Small Molecule Phikan5086
authors A.C.Joerger, R.Wilcken, F.M.Boeckler, A.R.Fersht
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B
Fragment: Dna-Binding Domain, Residues 94-312
Synonym: Antigen Ny-Co-13, Phosphoprotein P53, Tumor Suppre
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.1725 R_Free 0.1974
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.980 71.170 104.960 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.52 Å
ligand P86, ZN enzyme
Primary referenceHalogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53., Wilcken R, Liu X, Zimmermann MO, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM, J Am Chem Soc. 2012 Apr 18;134(15):6810-8. Epub 2012 Apr 5. PMID:22439615
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (4agm.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (4agm.pdb2.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 4AGM
  • CSU: Contacts of Structural Units for 4AGM
  • Structure Factors (3889 Kb)
  • Retrieve 4AGM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AGM from S2C, [Save to disk]
  • Re-refined 4agm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AGM 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 4AGM
  • 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 4AGM, from MSDmotif at EBI
  • Fold representative 4agm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4agm_A] [4agm_B] [4agm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4AGM with the sequences similar proteins can be viewed for 4AGM'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 4AGM
  • Community annotation for 4AGM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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