5IUC Sugar Binding Protein date Mar 17, 2016
title Crystal Structure Of The Gspb Siglec Domain With Sialyl T An Bound
authors L.V.Loukachevitch, K.P.Fialkowski, Z.Wawrzak, T.M.Iverson
compound source
Molecule: Platelet Binding Protein Gspb
Chain: A, B
Fragment: Binding Region, Siglec Domain
Synonym: Serine-Rich Adhesin For Platelets,Serine-Rich Repe Gspb;
Engineered: Yes
 Organism_scientific: Streptococcus Gordonii
Organism_taxid: 1302
Gene: Gspb
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbg101
symmetry Space Group: P 21 21 2
R_factor 0.156 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.670 66.547 55.854 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.25 Å
ligand A2G, GAL, MG, SIA enzyme
note 5IUC supersedes 4I8E, 3QD1
Primary referenceA Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors., Pyburn TM, Bensing BA, Xiong YQ, Melancon BJ, Tomasiak TM, Ward NJ, Yankovskaya V, Oliver KM, Cecchini G, Sulikowski GA, Tyska MJ, Sullam PM, Iverson TM, PLoS Pathog. 2011 Jul;7(7):e1002112. Epub 2011 Jul 7. PMID:21765814
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (5iuc.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (5iuc.pdb2.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 5IUC
  • CSU: Contacts of Structural Units for 5IUC
  • Structure Factors (844 Kb)
  • Retrieve 5IUC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IUC from S2C, [Save to disk]
  • Re-refined 5iuc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5IUC 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 5IUC
  • 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: [5iuc] [5iuc_A] [5iuc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5IUC
  • Community annotation for 5IUC at PDBWiki (http://pdbwiki.org)

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