3NDA Hydrolase Inhibitor date Jun 07, 2010
title Crystal Structure Of Serpin From Tick Ixodes Ricinus
authors P.Rezacova, Z.Kovarova, J.Chmelar, M.Mares
compound source
Molecule: Serpin-2
Chain: A, B
Engineered: Yes
 Organism_scientific: Ixodes Ricinus
Organism_common: Sheep Tick
Organism_taxid: 34613
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Like
symmetry Space Group: P 43
R_factor 0.171 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.575 84.575 124.412 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 1PE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • serine-type endopeptidase in...


    • Primary referenceA tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation., Chmelar J, Oliveira CJ, Rezacova P, Francischetti IM, Kovarova Z, Pejler G, Kopacek P, Ribeiro JM, Mares M, Kopecky J, Kotsyfakis M, Blood. 2010 Oct 12. PMID:20940421
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (199 Kb) [Save to disk]
  • Biological Unit Coordinates (3nda.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (3nda.pdb2.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 3NDA
  • CSU: Contacts of Structural Units for 3NDA
  • Structure Factors (1188 Kb)
  • Retrieve 3NDA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NDA from S2C, [Save to disk]
  • Re-refined 3nda structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NDA 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 3NDA
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3NDA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nda_A] [3nda_B] [3nda]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NDA: [SERPIN ] by SMART
    • Other resources with information on 3NDA
  • Community annotation for 3NDA 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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