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Open data
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Basic information
Entry | Database: PDB / ID: 6tte | ||||||
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Title | Beta-galactosidase in complex with PETG | ||||||
![]() | Beta-galactosidase![]() | ||||||
![]() | SUGAR BINDING PROTEIN / Bgal / ![]() | ||||||
Function / homology | ![]() alkali metal ion binding / lactose catabolic process / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saur, M. / Hartshorn, M.J. / Dong, J. / Reeks, J. / Bunkoczi, G. / Jhoti, H. / Williams, P.A. | ||||||
![]() | ![]() Title: Fragment-based drug discovery using cryo-EM. Authors: Michael Saur / Michael J Hartshorn / Jing Dong / Judith Reeks / Gabor Bunkoczi / Harren Jhoti / Pamela A Williams / ![]() 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. ...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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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 832 KB | Display | ![]() |
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PDB format | ![]() | 673.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10574MC ![]() 6tshC ![]() 6tskC ![]() 6ttfC ![]() 6tthC ![]() 6ttiC ![]() 6ttqC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data #1: Data from EPU (movies have been converted to compressed TIF) [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | ![]() Mass: 118395.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8VNN2, UniProt: P00722*PLUS, ![]() #2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-PTQ / #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Beta-galactosidase![]() |
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Molecular weight | Value: 0.464 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() ![]() |
Buffer solution | pH: 6.8 |
Specimen | Conc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Average exposure time: 59.98 sec. / Electron dose: 65.53 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 562 |
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Processing
EM software | Name: RELION / Version: 3.04 / Category: 3D reconstruction![]() |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 136013 |
Symmetry | Point symmetry![]() ![]() |
3D reconstruction![]() | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49895 / Symmetry type: POINT |