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
A, B

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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