4DOM Signaling Protein date Feb 09, 2012
title Crystal Structure Of The Tir-Domain Of Human Myeloid Differe Primary Response Protein (Myd88)
authors J.S.Jiang, G.A.Snyder, T.Xiao
compound source
Molecule: Myeloid Differentiation Primary Response Protein
Chain: A
Fragment: Tir Domain, Unp Residues 157-296
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Myd88
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.216
length a length b length c angle alpha angle beta angle gamma
33.415 57.991 62.495 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CSO, MLY enzyme

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] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (4dom.pdb1.gz) 27 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
  • 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 4DOM, from MSDmotif at EBI
  • Fold representative 4dom from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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