2VA5 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.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 Pro Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2;
Ec: 3.4.23.46
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
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 0.228 R_Free 0.319
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.138 102.138 168.258 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.75 Å
ligand C8C, 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] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2va5.pdb1.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 2VA5
  • CSU: Contacts of Structural Units for 2VA5
  • Likely Quarternary Molecular Structure file(s) for 2VA5
  • Structure Factors (192 Kb)
  • Retrieve 2VA5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VA5 from S2C, [Save to disk]
  • Re-refined 2va5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VA5 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 2VA5
  • 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 2VA5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m2va5, region A:45-119 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2va5_A] [2va5]
  • 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 2VA5
  • Community annotation for 2VA5 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