5YKL Antimicrobial Protein date Oct 15, 2017
title Antimicrobial Peptide Ay1c Designed From The Skin Secretion Odorous Frogs
authors I.Pal, H.S.Atreya, A.Bhunia
compound source
Molecule: Designed Ay1c
Chain: A
Engineered: Yes
Other_details: Designed Antimicrobial Peptide
 Synthetic: Yes
Organism_scientific: Odorrana Andersonii
Organism_taxid: 369514
methodSolution NMR
Primary referenceA Peptide-Nanoparticle System with Improved Efficacy against Multidrug Resistant Bacteria., Pal I, Bhattacharyya D, Kar RK, Zarena D, Bhunia A, Atreya HS, Sci Rep. 2019 Mar 14;9(1):4485. doi: 10.1038/s41598-019-41005-7. PMID:30872680
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (5ykl.pdb1.gz) 7 Kb
  • CSU: Contacts of Structural Units for 5YKL
  • Original NMR restraints for 5YKL from PDB
  • Retrieve 5YKL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YKL from S2C, [Save to disk]
    • View 5YKL 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 5YKL
  • 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: [5ykl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5YKL
  • Community annotation for 5YKL at PDBWiki (http://pdbwiki.org)

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