6TSK

Beta-galactosidase in complex with L-ribose


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.

(2020) Drug Discov Today 25: 485-490

  • DOI: 10.1016/j.drudis.2019.12.006
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidaseA, B, C, D1040Escherichia coliMutation(s): 0 
Gene Names: lacZ
EC: 3.2.1.23
Find proteins for L0N6M2 (Human alphaherpesvirus 1 strain RH2)
Explore L0N6M2 
Go to UniProtKB:  L0N6M2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0MK
Query on 0MK

Download CCD File 
A, B, C, D
beta-L-ribopyranose
C5 H10 O5
SRBFZHDQGSBBOR-FCAWWPLPSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2020-03-25
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary