3NKK Hydrolase date Jun 20, 2010
title Trypsin In Complex With Fluorine Containing Fragment
authors N.Schiering, A.Vulpetti, C.Dalvit
compound source
Molecule: Cationic Trypsin
Chain: A
Synonym: Beta-Trypsin, Alpha-Trypsin Chain 1, Alpha-Trypsin
Ec: 3.4.21.4
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.131 R_Free 0.148
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.423 58.088 66.579 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.12 Å
ligand CA, DMS, JLZ enzyme Hydrolase E.C.3.4.21.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCombined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments., Vulpetti A, Schiering N, Dalvit C, Proteins. 2010 Dec;78(16):3281-91. doi: 10.1002/prot.22836. PMID:20886466
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3nkk.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 3NKK
  • CSU: Contacts of Structural Units for 3NKK
  • Structure Factors (580 Kb)
  • Retrieve 3NKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NKK from S2C, [Save to disk]
  • Re-refined 3nkk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NKK 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 3NKK
  • 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 3NKK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nkk] [3nkk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NKK: [Tryp_SPc ] by SMART
  • Other resources with information on 3NKK
  • Community annotation for 3NKK 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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