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 1.4 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: https://doi.org/10.1016/j.drudis.2019.12.006
  • Primary Citation of Related Structures:  
    6TSH, 6TSK, 6TTE, 6TTF, 6TTH, 6TTI, 6TTQ

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,040Escherichia coliMutation(s): 0 
Gene Names: lacZ
EC: 3.2.1.23
UniProt
Find proteins for L0N6M2 (Human alphaherpesvirus 1 strain RH2)
Explore L0N6M2 
Go to UniProtKB:  L0N6M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0N6M2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0MK (Subject of Investigation/LOI)
Query on 0MK

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
beta-L-ribopyranose
C5 H10 O5
SRBFZHDQGSBBOR-FCAWWPLPSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.04

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-05-22
    Changes: Data collection, Database references, Refinement description