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
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
  • Alignments of the sequence of 3QYM with the sequences similar proteins can be viewed for 3QYM'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 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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