2PNL Hydrolase date Apr 24, 2007
title Crystal Structure Of Vp4 Protease From Infectious Pancreatic Virus (Ipnv) In Space Group P1
authors M.Paetzel, J.Lee, A.R.Feldman, B.Delmas
compound source
Molecule: Protease Vp4
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Vp4tri (Residues 514-716)
Engineered: Yes
Mutation: Yes
 Organism_scientific: Infectious Pancreatic Necrosis Virus
Organism_taxid: 11002
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 1
R_factor 0.190 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.703 69.262 191.388 93.06 95.03 97.56
method X-Ray Diffractionresolution 2.21 Å
ligand GAI, MSE enzyme
note 2PNL is a representative structure
Primary referenceCrystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction., Lee J, Feldman AR, Delmas B, Paetzel M, J Biol Chem. 2007 Aug 24;282(34):24928-37. Epub 2007 Jun 6. PMID:17553791
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (338 Kb) [Save to disk]
  • Biological Unit Coordinates (2pnl.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (2pnl.pdb2.gz) 39 Kb
  • Biological Unit Coordinates (2pnl.pdb3.gz) 38 Kb
  • Biological Unit Coordinates (2pnl.pdb4.gz) 37 Kb
  • Biological Unit Coordinates (2pnl.pdb5.gz) 38 Kb
  • Biological Unit Coordinates (2pnl.pdb6.gz) 37 Kb
  • Biological Unit Coordinates (2pnl.pdb7.gz) 37 Kb
  • Biological Unit Coordinates (2pnl.pdb8.gz) 39 Kb
  • Biological Unit Coordinates (2pnl.pdb9.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2PNL
  • CSU: Contacts of Structural Units for 2PNL
  • Likely Quarternary Molecular Structure file(s) for 2PNL
  • Structure Factors (3429 Kb)
  • Retrieve 2PNL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PNL from S2C, [Save to disk]
  • Re-refined 2pnl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2PNL 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 2PNL
  • 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
  • 3D motif for 2PNL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pnl_H] [2pnl_I] [2pnl_C] [2pnl_G] [2pnl_B] [2pnl_E] [2pnl_J] [2pnl_A] [2pnl_F] [2pnl] [2pnl_D]
  • SWISS-PROT database: [Q703G9]
  • Domain organization of [POLS_IPNVS] by SWISSPFAM
    • Other resources with information on 2PNL
  • Community annotation for 2PNL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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