3Q05 Antitumor Protein Dna date Dec 15, 2010
title An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics Sequence Specificity
authors T.J.Petty, T.D.Halazonetis
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B, C, D
Fragment: P53 Dna-Binding (Res 94-291) And Oligomerization 356) Domains;
Synonym: Antigen Ny-Co-13, Phosphoprotein P53, Tumor Suppre
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tp53, P53
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt5t

Molecule: Dna (26-Mer)
Chain: K
Engineered: Yes
Other_details: Tp53 Consensus Sequence Sense Strand Dna

Synthetic: Yes
Other_details: Consensus Human Tp53 Binding Sequence Sense

Molecule: Dna (26-Mer)
Chain: L
Engineered: Yes
Other_details: Tp53 Consensus Sequence Anti-Sense Strand Dn

Synthetic: Yes
Other_details: Consensus Human Tp53 Binding Sequence Anti-S Strand
symmetry Space Group: P 21 21 2
R_factor 0.238 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
163.298 169.764 55.664 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ZN enzyme
Primary referenceAn induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity., Petty TJ, Emamzadah S, Costantino L, Petkova I, Stavridi ES, Saven JG, Vauthey E, Halazonetis TD, EMBO J. 2011 Apr 26. PMID:21522129
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (3q05.pdb1.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 3Q05
  • CSU: Contacts of Structural Units for 3Q05
  • Structure Factors (491 Kb)
  • Retrieve 3Q05 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3Q05 from S2C, [Save to disk]
  • Re-refined 3q05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3Q05 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 3Q05
  • 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 3Q05, from MSDmotif at EBI
  • Fold representative 3q05 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3q05] [3q05_L] [3q05_C] [3q05_K] [3q05_D] [3q05_A] [3q05_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3Q05
  • Community annotation for 3Q05 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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