4DOM Crystal Structure of the TIR-domain of Human Myeloid Differentiation Primary Response protein (MyD88) date
authors Jiang, J.S., Snyder, G.A., Xiao, T.
compound source
symmetry
R_factor
R_Free 0.2157
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand CSO, MLY enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli., Snyder GA, Cirl C, Jiang J, Chen K, Waldhuber A, Smith P, Rommler F, Snyder N, Fresquez T, Durr S, Tjandra N, Miethke T, Xiao TS, Proc Natl Acad Sci U S A. 2013 Apr 8. PMID:23569230
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (4dom.pdb1.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 4DOM
  • CSU: Contacts of Structural Units for 4DOM
  • Structure Factors (80 Kb)
  • Retrieve 4DOM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DOM from S2C, [Save to disk]
  • Re-refined 4dom structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DOM 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 4DOM
  • 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 4DOM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dom_A] [4dom]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DOM: [TIR ] by SMART
  • Other resources with information on 4DOM
  • Community annotation for 4DOM at PDBWiki (http://pdbwiki.org)

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