5BQD Transcription date May 28, 2015
title Crystal Structure Of Tbx5 (1-239) Dimer
authors L.Pradhan, S.Gopal, A.Patel, H.Kasahara, H.J.Nam
compound source
Molecule: T-Box Transcription Factor Tbx5
Chain: A, B
Synonym: T-Box Protein 5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tbx5
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_variant: Ripl
symmetry Space Group: P 61 2 2
R_factor 0.246 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
81.455 81.455 341.022 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.58 Å
ligand MG enzyme
Primary referenceIntermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5., Pradhan L, Gopal S, Li S, Ashur S, Suryanarayanan S, Kasahara H, Nam HJ, Biochemistry. 2016 Mar 29;55(12):1702-10. doi: 10.1021/acs.biochem.6b00171. Epub , 2016 Mar 9. PMID:26926761
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (5bqd.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 5BQD
  • CSU: Contacts of Structural Units for 5BQD
  • Structure Factors (342 Kb)
  • Retrieve 5BQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BQD from S2C, [Save to disk]
  • Re-refined 5bqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BQD 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 5BQD
  • 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
  • Fold representative 5bqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bqd] [5bqd_B] [5bqd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5BQD: [TBOX ] by SMART
  • Other resources with information on 5BQD
  • Community annotation for 5BQD at PDBWiki (http://pdbwiki.org)

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