5EC5 Toxin date Oct 20, 2015
title Crystal Structure Of Lysenin Pore
authors M.Podobnik, P.Savory, N.Rojko, M.Kisovec, M.Bruce, L.Jayasinghe, G
compound source
Molecule: Lysenin
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S
Synonym: Efl1
Engineered: Yes
Mutation: Yes
Other_details: Protomer Of The Nonameric Pore
 Organism_scientific: Eisenia Fetida
Organism_common: Red Wiggler Worm
Organism_taxid: 6396
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
symmetry Space Group: P 43 21 2
R_factor 0.214 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
192.994 192.994 493.202 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand HG, MBO enzyme
Gene
Ontology
ChainFunctionProcessComponent
S, F, N, K, E, M, C, L, A, J, O, P, B, H, D, R, I, G
  • toxin activity


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (864 Kb) [Save to disk]
  • Biological Unit Coordinates (5ec5.pdb1.gz) 432 Kb
  • Biological Unit Coordinates (5ec5.pdb2.gz) 435 Kb
  • LPC: Ligand-Protein Contacts for 5EC5
  • CSU: Contacts of Structural Units for 5EC5
  • Structure Factors (2656 Kb)
  • Retrieve 5EC5 in mmCIF format [Save to disk]
  • Re-refined 5ec5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5EC5 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 5EC5
  • 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: [5ec5_C] [5ec5_L] [5ec5_S] [5ec5] [5ec5_J] [5ec5_R] [5ec5_M] [5ec5_A] [5ec5_K] [5ec5_F] [5ec5_H] [5ec5_E] [5ec5_N] [5ec5_P] [5ec5_O] [5ec5_I] [5ec5_D] [5ec5_G] [5ec5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5EC5
  • Community annotation for 5EC5 at PDBWiki (http://pdbwiki.org)

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