1BY8 Hydrolase date Oct 27, 1998
title The Crystal Structure Of Human Procathepsin K
authors J.M.Lalonde, B.Zhao, W.W.Smith, C.A.Janson, R.L.Desjarlais, T.A.T T.J.Carr, S.K.Thompson, D.S.Yamashita, D.F.Veber, S.S.Abdel-Meq
compound source
Molecule: Protein (Procathepsin K)
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.214 R_Free 0.344
length a length b length c angle alpha angle beta angle gamma
56.780 156.550 96.260 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1AU0, 1AU3

Primary referenceThe crystal structure of human procathepsin K., LaLonde JM, Zhao B, Janson CA, D'Alessio KJ, McQueney MS, Orsini MJ, Debouck CM, Smith WW, Biochemistry 1999 Jan 19;38(3):862-9. PMID:9893980
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (1by8.pdb1.gz) 46 Kb
  • CSU: Contacts of Structural Units for 1BY8
  • Likely Quarternary Molecular Structure file(s) for 1BY8
  • Retrieve 1BY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BY8 from S2C, [Save to disk]
  • View 1BY8 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 1BY8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1BY8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1by8a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1by8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1by8] [1by8_A]
  • SWISS-PROT database: [P43235]
  • Domain organization of [CATK_HUMAN] by SWISSPFAM
  • Domains found in 1BY8: [Inhibitor_I29] [Pept_C1 ] by SMART
  • Other resources with information on 1BY8
  • Community annotation for 1BY8 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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