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 Diffraction	resolution	2.20 Å
ligand	MG, PE4	enzyme
note	2X6V is a representative structure
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_D] SWISS-PROT database: Domain organization of by SWISSPFAM 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)

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