3QYM Transcription Activator Dna date Mar 03, 2011
title Structure Of P63 Dna Binding Domain In Complex With A 10 Bas Rich Response Element Half Site
authors O.Herzberg, C.Chen
compound source
Molecule: Tumor Protein 63
Chain: A, B, C, D, E, F, G, H
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 2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Apapapcpaptpgptptpt)-3'
Chain: I, J, K, L, M, N, O, P
Engineered: Yes
Other_details: Half Site Response Element

Synthetic: Yes
Other_details: Contains A Consensus P63 Binding Motif
symmetry Space Group: C 1 2 1
R_factor 0.245 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.872 180.198 104.379 90.00 92.62 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


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] (601 Kb) [Save to disk]
  • Biological Unit Coordinates (3qym.pdb1.gz) 298 Kb
  • Biological Unit Coordinates (3qym.pdb2.gz) 297 Kb
  • Biological Unit Coordinates (3qym.pdb3.gz) 300 Kb
  • LPC: Ligand-Protein Contacts for 3QYM
  • CSU: Contacts of Structural Units for 3QYM
  • Structure Factors (773 Kb)
  • Retrieve 3QYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QYM from S2C, [Save to disk]
  • Re-refined 3qym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QYM 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 3QYM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3QYM, from MSDmotif at EBI
  • Fold representative 3qym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qym_G] [3qym_I] [3qym_O] [3qym_P] [3qym_F] [3qym_H] [3qym_C] [3qym_E] [3qym_D] [3qym] [3qym_A] [3qym_L] [3qym_N] [3qym_M] [3qym_B] [3qym_K] [3qym_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3QYM
  • Community annotation for 3QYM 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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