5FV9 Transferase date Feb 03, 2016
title Crystal Structure Of Galnac-T2 In Complex With Compound 16d
authors M.Ghirardello, M.Rivas, A.Lacetera, I.Delso, E.Lira-Navarrete, T. S.Martin-Santamaria, R.Hurtado-Guerrero, P.Merino
compound source
Molecule: Galnac-T2
Chain: A, B, C, D, E, F
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_variant: X33
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppiczalphaa
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.493 121.748 250.155 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.07 Å
ligand EDO, GOL, MN, UDP, Y6W enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceGlycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates., Ghirardello M, de Las Rivas M, Lacetera A, Delso I, Lira-Navarrete E, Tejero T, Martin-Santamaria S, Hurtado-Guerrero R, Merino P, Chemistry. 2016 May 17;22(21):7215-24. doi: 10.1002/chem.201600467. Epub 2016 Apr, 13. PMID:27071848
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (985 Kb) [Save to disk]
  • Biological Unit Coordinates (5fv9.pdb1.gz) 321 Kb
  • Biological Unit Coordinates (5fv9.pdb2.gz) 333 Kb
  • Biological Unit Coordinates (5fv9.pdb3.gz) 336 Kb
  • Biological Unit Coordinates (5fv9.pdb4.gz) 336 Kb
  • LPC: Ligand-Protein Contacts for 5FV9
  • CSU: Contacts of Structural Units for 5FV9
  • Structure Factors (12039 Kb)
  • Retrieve 5FV9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FV9 from S2C, [Save to disk]
  • Re-refined 5fv9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5FV9 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 5FV9
  • 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: [5fv9_F] [5fv9_E] [5fv9_B] [5fv9_A] [5fv9] [5fv9_D] [5fv9_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5FV9: [RICIN ] by SMART
    • Other resources with information on 5FV9
  • Community annotation for 5FV9 at PDBWiki (http://pdbwiki.org)

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