5LKC Viral Protein date Jul 22, 2016
title Protruding Domain Of Gii.17 Norovirus Kawasaki308 In Complex Type A (Triglycan)
authors B.K.Singh, V.Morozov, G.S.Hansman
compound source
Molecule: Major Capsid Protein
Chain: A, B
Fragment: P Domain (Unp Residues 225-530)
Synonym: Major Viral Capsid Protein
Engineered: Yes
 Organism_scientific: Norovirus Gii
Organism_taxid: 122929
Gene: Vp1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Mbp-Htshp
symmetry Space Group: P 21 21 21
R_factor 0.153 R_Free 0.183
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.870 86.730 97.440 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand A2G, EDO, FUC, GLA, MG enzyme
Primary referenceHuman norovirus inhibition by a human milk oligosaccharide., Koromyslova A, Tripathi S, Morozov V, Schroten H, Hansman GS, Virology. 2017 May 12;508:81-89. doi: 10.1016/j.virol.2017.04.032. PMID:28505592
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (295 Kb) [Save to disk]
  • Biological Unit Coordinates (5lkc.pdb1.gz) 288 Kb
  • LPC: Ligand-Protein Contacts for 5LKC
  • CSU: Contacts of Structural Units for 5LKC
  • Structure Factors (554 Kb)
  • Retrieve 5LKC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LKC from S2C, [Save to disk]
  • Re-refined 5lkc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5LKC 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 5LKC
  • 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: [5lkc_A] [5lkc] [5lkc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5LKC
  • Community annotation for 5LKC at PDBWiki (http://pdbwiki.org)

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