3DM6 Hydrolase date Jun 30, 2008
title Beta-Secretase 1 Complexed With Statine-Based Inhibitor
authors J.Lindberg, N.Borkakoti, S.Nystrom
compound source
Molecule: Beta-Secretase 1
Chain: A, B, C
Fragment: Residues In Database 42-446
Synonym: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Enzyme 1, Membrane- Associated Aspartic Protease 2, Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
83.435 103.017 103.110 90.00 103.50 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 757, IPA BindingDB enzyme Hydrolase E.C. BRENDA
A, C, B

Primary referenceDesign, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues., Back M, Nyhlen J, Kvarnstrom I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nystrom S, Hallberg A, Rosenquist S, Samuelsson B, Bioorg Med Chem. 2008 Nov 1;16(21):9471-86. Epub 2008 Sep 19. PMID:18842420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (188 Kb) [Save to disk]
  • Biological Unit Coordinates (3dm6.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3dm6.pdb2.gz) 64 Kb
  • Biological Unit Coordinates (3dm6.pdb3.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 3DM6
  • CSU: Contacts of Structural Units for 3DM6
  • Likely Quarternary Molecular Structure file(s) for 3DM6
  • Structure Factors (774 Kb)
  • Retrieve 3DM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DM6 from S2C, [Save to disk]
  • Re-refined 3dm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DM6 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 3DM6
  • 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 3DM6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dm6_C] [3dm6] [3dm6_A] [3dm6_B]
  • SWISS-PROT database: [P56817]
  • Belongs to the β-amyloid cleaving enzyme (bace1) family according to TCDB.
  • Domain organization of [BACE1_HUMAN] by SWISSPFAM
  • Other resources with information on 3DM6
  • Community annotation for 3DM6 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science