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- PDB-8p1t: Crystal structure of human methionine adenosyltransferase 2A (MAT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p1t | ||||||
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Title | Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Z237451470 | ||||||
![]() | S-adenosylmethionine synthase isoform type-2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Thieulin-Pardo, G. / Neumann, L. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of novel methionine adenosyltransferase 2A (MAT2A) allosteric inhibitors by structure-based virtual screening. Authors: Kalliokoski, T. / Kettunen, H. / Kumpulainen, E. / Kettunen, E. / Thieulin-Pardo, G. / Neumann, L. / Thomsen, M. / Paul, R. / Malyutina, A. / Georgiadou, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8p1vC ![]() 8p1wC ![]() 8p4hC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 45703.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 425 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/WJL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/WJL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAM / ![]() | ||||||
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#3: Chemical | ChemComp-WJL / | ||||||
#4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-CL / | ![]() #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.3 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 0.10 M HEPES pH 8.0, 8 - 12%(v/v) Ethylene glycol, 8 - 10.0% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.44→54.98 Å / Num. obs: 67105 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.034 / Rsym value: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.44→1.47 Å / Rmerge(I) obs: 1.616 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3302 / CC1/2: 0.614 / Rpim(I) all: 0.568 / Rsym value: 1.511 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.442→54.976 Å
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Refine LS restraints |
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LS refinement shell |
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