6YDE Metal Binding Protein date Mar 20, 2020
title X-Ray Structure Of Lpmo
authors T.Tandrup, T.Tryfona, K.E.H.Frandsen, K.S.Johansen, P.Dupree, L.L
compound source
Molecule: Lpmo Lytic Polysaccharide Monooxygenase
Chain: A
Engineered: Yes
Organism_scientific: Collariella Virescens
Organism_taxid: 1934374
Gene: Aa9
Expression_system: Aspergillus Oryzae
Expression_system_taxid: 5062
symmetry Space Group: P 21 21 2
R_factor 0.194 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.550 124.370 51.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BGC, CU, HIC, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • monooxygenase activity


  • Primary referenceOligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases., Tandrup T, Tryfona T, Frandsen KEH, Johansen KS, Dupree P, Lo Leggio L, Biochemistry. 2020 Sep 15;59(36):3347-3358. doi: 10.1021/acs.biochem.0c00312., Epub 2020 Aug 27. PMID:32818374
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (6yde.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 6YDE
  • CSU: Contacts of Structural Units for 6YDE
  • Structure Factors (376 Kb)
  • Retrieve 6YDE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YDE from S2C, [Save to disk]
  • View 6YDE 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 6YDE
  • 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: [6yde_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6YDE
  • Community annotation for 6YDE at PDBWiki (http://pdbwiki.org)

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