3TDM Computationally designed TIM-barrel protein, HalfFLR date
authors Harp, J.M., Fortenberry, C., Bowman, E., Profitt, W., Dorr, B., Mizoue, L.
compound source
R_Free 0.288
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand PO4 enzyme
A, D, C, B

Primary referenceExploring symmetry as an avenue to the computational design of large protein domains., Fortenberry C, Bowman EA, Proffitt W, Dorr B, Combs S, Harp J, Mizoue L, Meiler J, J Am Chem Soc. 2011 Nov 16;133(45):18026-9. Epub 2011 Oct 21. PMID:21978247
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (3tdm.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (3tdm.pdb2.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 3TDM
  • CSU: Contacts of Structural Units for 3TDM
  • Structure Factors (277 Kb)
  • Retrieve 3TDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TDM from S2C, [Save to disk]
  • Re-refined 3tdm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TDM 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 3TDM
  • 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
  • 3D motif for 3TDM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tdm_C] [3tdm_A] [3tdm_B] [3tdm] [3tdm_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3TDM
  • Community annotation for 3TDM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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