3KZ8 Transcription Dna date Dec 08, 2009
title Diversity In Dna Recognition By P53 Revealed By Crystal Stru With Hoogsteen Base Pairs (P53-Dna Complex 3)
authors H.Rozenberg, O.Suad, Z.Shakked
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B
Fragment: P53 Core Domain, Unp Residues 94-293
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tp53
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet27-B

Molecule: Dna (5'- D(Tpgpgpgpcpaptpgpcpcpcpgpgpgpcpaptpgpcp 3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Fragment.
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.422 49.812 68.056 90.00 93.48 90.00
method X-Ray Diffractionresolution 1.91 Å
ligand IOD, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs., Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z, Nat Struct Mol Biol. 2010 Apr;17(4):423-9. Epub 2010 Apr 4. PMID:20364130
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (3kz8.pdb1.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 3KZ8
  • CSU: Contacts of Structural Units for 3KZ8
  • Structure Factors (277 Kb)
  • Retrieve 3KZ8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KZ8 from S2C, [Save to disk]
  • Re-refined 3kz8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KZ8 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 3KZ8
  • 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 3KZ8, from MSDmotif at EBI
  • Fold representative 3kz8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kz8_A] [3kz8_C] [3kz8] [3kz8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3KZ8 with the sequences similar proteins can be viewed for 3KZ8'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 3KZ8
  • Community annotation for 3KZ8 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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