3QYN Transcription Activator Dna date Mar 03, 2011
title Structure Of P63 Dna Binding Domain In Complex With A 22 Bas Rich Response Element Containing 2 Base Pair Spacer Between Sites
authors C.Chen, O.Herzberg
compound source
Molecule: Tumor Protein 63
Chain: A, B, C, D
Fragment: Dna Binding Domain (Unp Residues 166-362)
Synonym: P63, Chronic Ulcerative Stomatitis Protein, Cusp, Keratinocyte Transcription Factor Ket, Transformation-Relat 63, Tp63, Tumor Protein P73-Like, P73l, P40, P51;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ket, P63, P73h, P73l, Tp63, Tp73l
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta II (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Apapapcpaptpgptptptptpapapapa Gptptpt)-3';
Chain: E, F
Engineered: Yes
Other_details: Full Response Element With A 2-Base-Pair Spa

Synthetic: Yes
Other_details: Contains A Consensus P63 Binding Motif
symmetry Space Group: P 63
R_factor 0.210 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
140.984 140.984 119.346 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme
Primary referenceStructures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements., Chen C, Gorlatova N, Kelman Z, Herzberg O, Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6456-6461. Epub 2011 Apr 4. PMID:21464285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (308 Kb) [Save to disk]
  • Biological Unit Coordinates (3qyn.pdb1.gz) 300 Kb
  • LPC: Ligand-Protein Contacts for 3QYN
  • CSU: Contacts of Structural Units for 3QYN
  • Structure Factors (771 Kb)
  • Retrieve 3QYN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QYN from S2C, [Save to disk]
  • Re-refined 3qyn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QYN 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 3QYN
  • 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 3QYN, from MSDmotif at EBI
  • Fold representative 3qyn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qyn_D] [3qyn] [3qyn_C] [3qyn_E] [3qyn_B] [3qyn_F] [3qyn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3QYN with the sequences similar proteins can be viewed for 3QYN'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 3QYN
  • Community annotation for 3QYN 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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