1YK7 Hydrolase date Jan 17, 2005
title Cathepsin K Complexed With A Cyanopyrrolidine Inhibitor
authors D.G.Barrett, D.N.Deaton, A.M.Hassell, R.B.Mcfadyen, A.B.Miller, L.R.Miller, L.M.Shewchuk, F.X.Tavares, D.H.Willard, L.L.Wright
compound source
Molecule: Cathepsin K
Chain: A
Fragment: Mature Form Of Cathepsin K (Sequence Database Res 329);
Synonym: Cathepsin O, Cathepsin X, Cathepsin O2
Ec: 3.4.22.38
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctsk, Ctso, Ctso2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
32.241 66.653 93.187 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NBL enzyme Hydrolase E.C.3.4.22.38 BRENDA
related structures by homologous chain: 1AU3, 1NLJ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNovel and potent cyclic cyanamide-based cathepsin K inhibitors., Deaton DN, Hassell AM, McFadyen RB, Miller AB, Miller LR, Shewchuk LM, Tavares FX, Willard DH Jr, Wright LL, Bioorg Med Chem Lett. 2005 Apr 1;15(7):1815-9. PMID:15780613
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1yk7.pdb1.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 1YK7
  • CSU: Contacts of Structural Units for 1YK7
  • Likely Quarternary Molecular Structure file(s) for 1YK7
  • Structure Factors (55 Kb)
  • Retrieve 1YK7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YK7 from S2C, [Save to disk]
  • Re-refined 1yk7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YK7 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 1YK7
  • 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 1YK7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yk7] [1yk7_A]
  • SWISS-PROT database: [P43235]
  • Domain organization of [CATK_HUMAN] by SWISSPFAM
  • Domain found in 1YK7: [Pept_C1 ] by SMART
  • Other resources with information on 1YK7
  • Community annotation for 1YK7 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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