5N4D Hydrolase date Feb 10, 2017
title Prolyl Oligopeptidase B From Galerina Marginata Bound To 25m Macrocyclization Substrate - D661a Mutant
authors C.M.Czekster, S.A.Mcmahon, H.Ludewig, J.H.Naismith
compound source
Molecule: Prolyl Oligopeptidase
Chain: A, B
Engineered: Yes
Mutation: Yes
Organism_scientific: Galerina Marginata
Organism_taxid: 109633
Gene: Popb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Alpha-Amanitin Proprotein
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Galerina Marginata
Organism_taxid: 109633
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.040 114.880 141.310 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.62 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCharacterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates., Czekster CM, Ludewig H, McMahon SA, Naismith JH, Nat Commun. 2017 Oct 19;8(1):1045. doi: 10.1038/s41467-017-00862-4. PMID:29051530
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (5n4d.pdb1.gz) 137 Kb
  • Biological Unit Coordinates (5n4d.pdb2.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 5N4D
  • CSU: Contacts of Structural Units for 5N4D
  • Structure Factors (8382 Kb)
  • Retrieve 5N4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5N4D from S2C, [Save to disk]
  • View 5N4D 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 5N4D
  • 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: [5n4d_A] [5n4d_D] [5n4d_C] [5n4d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5N4D
  • Community annotation for 5N4D at PDBWiki (http://pdbwiki.org)

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