6TSH

Beta-galactosidase in complex with deoxygalacto-nojirimycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based drug discovery using cryo-EM.

Saur, M.Hartshorn, M.J.Dong, J.Reeks, J.Bunkoczi, G.Jhoti, H.Williams, P.A.

(2019) Drug Discov Today --: --

  • DOI: 10.1016/j.drudis.2019.12.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-ba ...

    Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-based drug discovery (FBDD) based on in-house method development. We demonstrate not only that cryo-EM can reveal details of the molecular interactions between fragments and a protein, but also that the current reproducibility, quality, and throughput are compatible with FBDD. We exemplify this using the test system β-galactosidase (Bgal) and the oncology target pyruvate kinase 2 (PKM2).


    Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK. Electronic address: harren.jhoti@astx.com.,Isohelio Ltd, Lewis House, Great Chesterford Court, Great Chesterford, CB10 1PF, UK.,Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
1040Escherichia coliMutation(s): 0 
Gene Names: lacZ
EC: 3.2.1.23
Find proteins for Q8VNN2 (Escherichia coli)
Go to UniProtKB:  Q8VNN2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DGJ
Query on DGJ

Download SDF File 
Download CCD File 
A, B, C, D
(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
1-deoxygalactonojirimycin
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Database references