2VA6 Hydrolase date Aug 30, 2007
title X-Ray Crystal Structure Of Beta Secretase Complexed With Com
authors P.D.Edwards, J.S.Albert, M.Sylvester, D.Aharony, D.Andisik, O.Cal J.B.Campbell, R.A.Carr, G.Chessari, M.Congreve, M.Frederickson, R.H.A.Folmer, S.Geschwindner, G.Koether, K.Kolmodin, J.Krumrine R.C.Mauger, C.W.Murray, L.L.Olsson, S.Patel, N.Spear, G.Tian
compound source
Molecule: Beta Secretase 1
Chain: A
Fragment: Protease Domain, Residues 14-453
Synonym: Beta-Site App Cleaving Enzyme 1, Beta-Site Amyloid Protein Cleaving Enzyme 1, Membrane -Associated Aspartic Pr Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2;
Ec: 3.4.23.46
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Organ: Brain
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 61 2 2
R_factor 0.224 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.971 102.971 167.280 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand H24, IOD BindingDB enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceApplication of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine beta-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency., Edwards PD, Albert JS, Sylvester M, Aharony D, Andisik D, Callaghan O, Campbell JB, Carr RA, Chessari G, Congreve M, Frederickson M, Folmer RH, Geschwindner S, Koether G, Kolmodin K, Krumrine J, Mauger RC, Murray CW, Olsson LL, Patel S, Spear N, Tian G, J Med Chem. 2007 Nov 29;50(24):5912-5925. Epub 2007 Nov 7. PMID:17985862
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (2va6.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 2VA6
  • CSU: Contacts of Structural Units for 2VA6
  • Likely Quarternary Molecular Structure file(s) for 2VA6
  • Structure Factors (255 Kb)
  • Retrieve 2VA6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VA6 from S2C, [Save to disk]
  • Re-refined 2va6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VA6 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 2VA6
  • 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 2VA6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2va6] [2va6_A]
  • 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 2VA6
  • Community annotation for 2VA6 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