3IGL Transcription Dna date Jul 28, 2009
title Diversity In Dna Recognition By P53 Revealed By Crystal Stru With Hoogsteen Base Pairs (P53-Dna Complex 1)
authors M.Kitayner, O.Suad, H.Rozenberg, 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
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(Cpgpgpgpcpaptpgpcpcpcpg)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Fragment.
symmetry Space Group: C 1 2 1
R_factor 0.148 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
137.161 49.841 33.962 90.00 93.96 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand EDO, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


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] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (3igl.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 3IGL
  • CSU: Contacts of Structural Units for 3IGL
  • Structure Factors (302 Kb)
  • Retrieve 3IGL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IGL from S2C, [Save to disk]
  • Re-refined 3igl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IGL 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 3IGL
  • 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 3IGL, from MSDmotif at EBI
  • Fold representative 3igl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3igl_A] [3igl] [3igl_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3IGL with the sequences similar proteins can be viewed for 3IGL'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 3IGL
  • Community annotation for 3IGL 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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