3WB5 Hydrolase date May 13, 2013
title Crystal Structure Of Beta Secetase In Complex With (6s)-2-Am Dimethyl-6-[(1r,2r)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydro 4-One
authors S.Yonezawa, K.Fujiwara, T.Yamamoto, K.Hattori, H.Yamakawa, C.Muto M.Hosono, Y.Tanaka, T.Nakano, H.Takemoto, M.Arisawa, S.Shuto
compound source
Molecule: Beta-Secretase 1
Chain: A
Fragment: Active Protease Domain, Unp Residues 43-454
Synonym: Aspartyl Protease 2, Asp2, Asp 2, Beta-Site Amyloi Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Memapsin-2, Membrane-Associated Aspartic Protease 2;
Ec: 3.4.23.46
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace1, Bace, Kiaa1149
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet28a
symmetry Space Group: P 61 2 2
R_factor 0.201 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.926 101.926 168.936 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand 0B4, DMS, GOL, IOD enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceConformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations., Yonezawa S, Fujiwara K, Yamamoto T, Hattori K, Yamakawa H, Muto C, Hosono M, Tanaka Y, Nakano T, Takemoto H, Arisawa M, Shuto S, Bioorg Med Chem. 2013 Aug 28. pii: S0968-0896(13)00730-X. doi:, 10.1016/j.bmc.2013.08.036. PMID:24051074
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (3wb5.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 3WB5
  • CSU: Contacts of Structural Units for 3WB5
  • Structure Factors (141 Kb)
  • Retrieve 3WB5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WB5 from S2C, [Save to disk]
  • Re-refined 3wb5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WB5 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 3WB5
  • 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 3WB5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wb5_A] [3wb5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3WB5
  • Community annotation for 3WB5 at PDBWiki (http://pdbwiki.org)

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