5A24 Hydrolase date May 12, 2015
title Crystal Structure Of Dionain-1, The Major Endopeptidase In The Venus Flytrap Digestive Juice
authors M.W.Risor, L.R.Thomsen, K.W.Sanggaard, T.A.Nielsen, I.B.Thogerse M.V.Lukassen, L.Rossen, I.Garcia-Ferrer, T.Guevara, E.Meinjohan N.C.Nielsen, F.X.Gomis-Ruth, J.J.Enghild
compound source
Molecule: Dionain-1
Chain: A
Fragment: Mature Enzyme
Engineered: Yes
Organism_scientific: Dionaea Muscipula
Organism_common: Venus Flytrap
Organism_taxid: 4362
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Km71h
Expression_system_plasmid: Ppiczalphac
Other_details: From The Plant Digestive Juice
symmetry Space Group: C 1 2 1
R_factor 0.1575 R_Free 0.1720
length a length b length c angle alpha angle beta angle gamma
73.850 47.790 57.790 90.00 92.44 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand E64, PO4 enzyme

Primary referenceEnzymatic and structural characterization of the major endopeptidase in the Venus flytrap digestion fluid., Risor MW, Thomsen LR, Sanggaard KW, Nielsen TA, Thogersen IB, Lukassen MV, Rossen L, Garcia-Ferrer I, Guevara T, Scavenius C, Meinjohanns E, Gomis-Ruth FX, Enghild JJ, J Biol Chem. 2015 Dec 1. pii: jbc.M115.672550. PMID:26627834
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (5a24.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5A24
  • CSU: Contacts of Structural Units for 5A24
  • Structure Factors (280 Kb)
  • Retrieve 5A24 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5A24 from S2C, [Save to disk]
  • Re-refined 5a24 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5A24 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 5A24
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5a24 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a24_A] [5a24]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5A24: [Pept_C1 ] by SMART
  • Other resources with information on 5A24
  • Community annotation for 5A24 at PDBWiki (http://pdbwiki.org)

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