2X6V Transcription Dna date Feb 22, 2010
title Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna- Free Form
authors D.Ptchelkine, C.U.Stirnimann, C.Grimm, C.W.Mueller
compound source
Molecule: T-Box Transcription Factor Tbx5
Chain: A, B
Fragment: T-Box Domain, Residues 51-251
Synonym: T-Box Protein 5, Human Tbx5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pprox Htb

Molecule: 5'-D(Tpcptpcpapcpapcpcptptp)-3'
Chain: C

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpapapgpgptpgptpgpapgp)-3'
Chain: D

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61 2 2
R_factor 0.1973 R_Free 0.2252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
118.240 118.240 243.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MG, PE4 enzyme
note 2X6V is a representative structure
Primary referenceStructural basis of TBX5-DNA recognition: the T-box domain in its DNA-bound and -unbound form., Stirnimann CU, Ptchelkine D, Grimm C, Muller CW, J Mol Biol. 2010 Jul 2;400(1):71-81. Epub 2010 May 5. PMID:20450920
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (2x6v.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 2X6V
  • CSU: Contacts of Structural Units for 2X6V
  • Structure Factors (394 Kb)
  • Retrieve 2X6V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X6V from S2C, [Save to disk]
  • Re-refined 2x6v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X6V 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 2X6V
  • 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 2X6V, from MSDmotif at EBI
  • Fold representative 2x6v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x6v_A] [2x6v_B] [2x6v_C] [2x6v] [2x6v_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2X6V: [TBOX ] by SMART
  • Alignments of the sequence of 2X6V with the sequences similar proteins can be viewed for 2X6V'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 2X6V
  • Community annotation for 2X6V 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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