3D05 Transcription date May 01, 2008
title Human P53 Core Domain With Hot Spot Mutation R249s (II)
authors O.Suad, H.Rozenberg, L.J.W.Shimon, F.Frolow, Z.Shakked
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A
Fragment: P53 Core Domain, Unp Residues 94-293
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
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet27-B
symmetry Space Group: P 65 2 2
R_factor 0.218 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.374 44.374 330.026 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand ZN enzyme
Primary referenceStructural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations., Suad O, Rozenberg H, Brosh R, Diskin-Posner Y, Kessler N, Shimon LJ, Frolow F, Liran A, Rotter V, Shakked Z, J Mol Biol. 2009 Jan 9;385(1):249-65. Epub 2008 Oct 30. PMID:18996393
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (3d05.pdb1.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 3D05
  • CSU: Contacts of Structural Units for 3D05
  • Likely Quarternary Molecular Structure file(s) for 3D05
  • Structure Factors (321 Kb)
  • Retrieve 3D05 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D05 from S2C, [Save to disk]
  • Re-refined 3d05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D05 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 3D05
  • 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 3D05, from MSDmotif at EBI
  • Fold representative 3d05 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d05_A] [3d05]
  • SWISS-PROT database: [P04637]
  • Belongs to the pore-forming pnc-27 peptide of 32 aas from the p53 tumor suppressor protein (pnc-27) family according to TCDB.
  • Domain organization of [P53_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3D05 with the sequences similar proteins can be viewed for 3D05'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 3D05
  • Community annotation for 3D05 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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