1Y5A Hydrolase date Dec 02, 2004
title Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibit Complex With Bovine Trypsin Mutant
authors A.Di Fenza, A.Heine, G.Klebe
compound source
Molecule: Trypsin, Cationic
Chain: T
Synonym: Beta-Trypsin
Engineered: Yes
Mutation: Yes
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: P 31 2 1
length a length b length c angle alpha angle beta angle gamma
54.779 54.779 108.576 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.40 Å
ligand CA, GOL, IMD, SO4, TL2 enzyme Hydrolase E.C. BRENDA

Primary referenceUnderstanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions., Di Fenza A, Heine A, Koert U, Klebe G, ChemMedChem. 2007 Mar;2(3):297-308. PMID:17191291
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1y5a.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 1Y5A
  • CSU: Contacts of Structural Units for 1Y5A
  • Likely Quarternary Molecular Structure file(s) for 1Y5A
  • Structure Factors (293 Kb)
  • Retrieve 1Y5A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y5A from S2C, [Save to disk]
  • Re-refined 1y5a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y5A 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 1Y5A
  • 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
  • 3D motif for 1Y5A, from MSDmotif at EBI
  • Fold representative 1y5a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y5a] [1y5a_T]
  • SWISS-PROT database: [P00760]
  • Domain organization of [TRY1_BOVIN] by SWISSPFAM
  • Domain found in 1Y5A: [Tryp_SPc ] by SMART
  • Other resources with information on 1Y5A
  • Community annotation for 1Y5A 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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