5QBV Hydrolase date Aug 17, 2017
title Crystal Structure Of Human Cathepsin-S With Bound Ligand
authors S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burl
compound source
Molecule: Cathepsin S
Chain: A, B
Ec: 3.4.22.27
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctss
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: C 1 2 1
R_factor 0.147 R_Free 0.172
crystal
cell
length a length b length c angle alpha angle beta angle gamma
172.391 34.311 104.021 90.00 125.27 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand N2D enzyme Hydrolase E.C.3.4.22.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiazinones as P2 replacements for pyrazole-based cathepsin S inhibitors., Ameriks MK, Bembenek SD, Burdett MT, Choong IC, Edwards JP, Gebauer D, Gu Y, Karlsson L, Purkey HE, Staker BL, Sun S, Thurmond RL, Zhu J, Bioorg Med Chem Lett. 2010 Jul 15;20(14):4060-4. Epub 2010 May 25. PMID:20541404
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (5qbv.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (5qbv.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 5QBV
  • CSU: Contacts of Structural Units for 5QBV
  • Structure Factors (991 Kb)
  • Retrieve 5QBV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5QBV from S2C, [Save to disk]
  • View 5QBV 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 5QBV
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5qbv_B] [5qbv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5QBV
  • Community annotation for 5QBV at PDBWiki (http://pdbwiki.org)

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