5VYB Sugar Binding Protein date May 24, 2017
title Structure Of The Carbohydrate Recognition Domain Of Dectin-2 With A Mammalian-Type High Mannose Man9glcnac2 Oligosacchar
authors H.Feinberg, S.A.F.Jegouzo, M.J.Rex, K.Drickamer, M.E.Taylor, W.I.
compound source
Molecule: C-Type Lectin Domain Family 6 Member A
Chain: A
Synonym: C-Type Lectin Superfamily Member 10,Dendritic Cell Associated C-Type Lectin 2,Dectin-2;
Engineered: Yes
Other_details: The N-Terminal Ala Is A Result Of Cloning
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Clec6a, Clecsf10, Dectin2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: C 2 2 21
R_factor 0.205 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.055 78.834 76.459 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand BMA, CA, MAN, NA, PEG enzyme
Primary referenceMechanism of pathogen recognition by human dectin-2., Feinberg H, Jegouzo SAF, Rex MJ, Drickamer K, Weis WI, Taylor ME, J Biol Chem. 2017 Aug 11;292(32):13402-13414. doi: 10.1074/jbc.M117.799080. Epub , 2017 Jun 26. PMID:28652405
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (5vyb.pdb1.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 5VYB
  • CSU: Contacts of Structural Units for 5VYB
  • Structure Factors (66 Kb)
  • Retrieve 5VYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VYB from S2C, [Save to disk]
  • Re-refined 5vyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VYB 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 5VYB
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vyb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VYB
  • Community annotation for 5VYB at PDBWiki (http://pdbwiki.org)

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