6TSH

Beta-galactosidase in complex with deoxygalacto-nojirimycin

• PDB DOI: https://doi.org/10.2210/pdb6TSH/pdb
• EM Map EMD-10563: EMDB EMDataResource

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-20 Released: 2020-01-08 
• Deposition Author(s): Saur, M., Hartshorn, M.J., Dong, J., Reeks, J., Bunkoczi, G., Jhoti, H., Williams, P.A.

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Experimental Data Snapshot

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

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

• PubMed: 31877353 
• 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).

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Organizational Affiliation: 

Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 474.33 kDa 
• Atom Count: 33,536 
• Modelled Residue Count: 4,060 
• Deposited Residue Count: 4,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,040	Escherichia coli	Mutation(s): 0  Gene Names: lacZ EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGJ (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol C6 H13 N O4 LXBIFEVIBLOUGU-DPYQTVNSSA-N
MG	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:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.04

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-08 
Deposition Author(s): Saur, M., Hartshorn, M.J., Dong, J., Reeks, J., Bunkoczi, G., Jhoti, H., Williams, P.A.

Revision History  

• Version 1.0: 2020-01-08
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2020-03-25
  Changes: Database references
• Version 1.3: 2024-05-22
  Changes: Data collection, Database references, Refinement description