2PCX Transcription date Mar 30, 2007
title Crystal Structure Of P53dbd(R282q) At 1.54-Angstrom Resolution
authors C.Tu, G.Shaw, X.Ji
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A
Fragment: P53 Dbd Domain
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13;
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tp53, P53
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet17b(+)
symmetry Space Group: P 1
R_factor 0.191 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.900 35.200 41.600 111.80 94.90 112.40
method X-Ray Diffractionresolution 1.54 Å
ligand ZN enzyme
Primary referenceImpact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution., Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X, Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):471-7. Epub 2008, Apr 19. PMID:18453682
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (2pcx.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2PCX
  • CSU: Contacts of Structural Units for 2PCX
  • Likely Quarternary Molecular Structure file(s) for 2PCX
  • Structure Factors (314 Kb)
  • Retrieve 2PCX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PCX from S2C, [Save to disk]
  • Re-refined 2pcx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2PCX 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 2PCX
  • 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 2PCX, from MSDmotif at EBI
  • Fold representative 2pcx from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pcx_A]
  • SWISS-PROT database: [P04637]
  • Domain organization of [P53_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2PCX with the sequences similar proteins can be viewed for 2PCX's classification [P53_HUMAN] 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 [P53_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2PCX
  • Community annotation for 2PCX 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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