6B8O Signaling Protein date Oct 09, 2017
title Wt Ig-Like V Domain With Phosphatidylserine
authors A.Sudom, Z.Wang
compound source
Molecule: Triggering Receptor Expressed On Myeloid Cells 2
Chain: A, B, C, D, E, F
Synonym: Trem-2,Triggering Receptor Expressed On Monocytes
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trem2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
symmetry Space Group: P 41 21 2
R_factor 0.222 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.331 160.331 86.205 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO, IOD, NAG, PSF, SO4 enzyme
Primary referenceMolecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2., Sudom A, Talreja S, Danao J, Bragg E, Kegel R, Min X, Sharkov N, Marcora E, Thibault S, Bradley J, Wood S, Lim AC, Chen H, Wang S, Foltz IN, Sambashivan S, Wang Z, J Biol Chem. 2018 May 24. pii: RA118.002352. doi: 10.1074/jbc.RA118.002352. PMID:29794134
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (6b8o.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 6B8O
  • CSU: Contacts of Structural Units for 6B8O
  • Structure Factors (2408 Kb)
  • Retrieve 6B8O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6B8O from S2C, [Save to disk]
    • View 6B8O 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 6B8O
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6b8o_C] [6b8o_F] [6b8o_E] [6b8o_D] [6b8o_A] [6b8o_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6B8O
  • Community annotation for 6B8O at PDBWiki (http://pdbwiki.org)

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