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
crystal
cell
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
Gene
Ontology
ChainFunctionProcessComponent
A


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)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science