5IE1 Hydrolase date Feb 24, 2016
title Crystal Structure Of Bace1 In Complex With 3-(2-Amino-6-(O-T Quinolin-3-Yl)-N-(3,3-Dimethylbutyl)Propanamide
authors J.B.Jordan, D.A.Whittington, M.D.Bartberger, E.A.Sickmier, K.Che Y.Cheng, T.Judd
compound source
Molecule: Beta-Secretase 1
Chain: A
Fragment: Unp Residues 43-453
Synonym: Aspartyl Protease 2,Asp 2,Beta-Site Amyloid Precur Protein Cleaving Enzyme 1,Beta-Site App Cleaving Enzyme 1,M 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: Enterobacteria Phage L1
Expression_system_taxid: 268588
symmetry Space Group: P 61 2 2
R_factor 0.214 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.494 102.494 169.348 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 6BS, GOL, IOD enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceFragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of beta-Secretase., Jordan JB, Whittington DA, Bartberger MD, Sickmier EA, Chen K, Cheng Y, Judd T, J Med Chem. 2016 Apr 28;59(8):3732-49. doi: 10.1021/acs.jmedchem.5b01917. Epub, 2016 Apr 6. PMID:26978477
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5ie1.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5IE1
  • CSU: Contacts of Structural Units for 5IE1
  • Structure Factors (377 Kb)
  • Retrieve 5IE1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IE1 from S2C, [Save to disk]
  • Re-refined 5ie1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IE1 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 5IE1
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r5ie1, region E:82-181 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ie1_A] [5ie1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5IE1
  • Community annotation for 5IE1 at PDBWiki (http://pdbwiki.org)

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