4IBU Dna Binding Protein Dna date Dec 09, 2012
title Human P53 Core Domain With Hot Spot Mutation R273c And Secon Suppressor Mutation T284r In Sequence-Specific Complex With
authors A.Eldar, H.Rozenberg, Y.Diskin-Posner, Z.Shakked
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B, C, D
Fragment: Dna Binding Domain
Synonym: Antigen Ny-Co-13, Phosphoprotein P53, Tumor Suppre
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: P53, Tp53
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-27-B

Molecule: Dna (5'-D(Cpgpgpgpcpaptpgpcpcpcpg)-3'
Chain: E, F, G, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1
R_factor 0.163 R_Free 0.197
length a length b length c angle alpha angle beta angle gamma
54.537 58.158 77.968 82.96 87.78 73.57
method X-Ray Diffractionresolution 1.70 Å
ligand ACT, EDO, ZN enzyme
A, D, C, B

Primary referenceStructural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions., Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z, Nucleic Acids Res. 2013 Jul 17. PMID:23863845
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (318 Kb) [Save to disk]
  • Biological Unit Coordinates (4ibu.pdb1.gz) 306 Kb
  • LPC: Ligand-Protein Contacts for 4IBU
  • CSU: Contacts of Structural Units for 4IBU
  • Structure Factors (1502 Kb)
  • Retrieve 4IBU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IBU from S2C, [Save to disk]
  • Re-refined 4ibu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IBU 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 4IBU
  • 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 4IBU, from MSDmotif at EBI
  • Fold representative 4ibu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ibu_D] [4ibu_C] [4ibu_H] [4ibu_F] [4ibu_G] [4ibu_A] [4ibu_B] [4ibu_E] [4ibu]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IBU
  • Community annotation for 4IBU at PDBWiki (http://pdbwiki.org)

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