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- PDB-8p4h: Crystal structure of human methionine adenosyltransferase 2A (MAT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p4h | ||||||
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Title | Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric compound IDEAYA cmpd A | ||||||
![]() | 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 | ![]() | 627.2 KB | Display | ![]() |
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PDB format | ![]() | 513.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8p1tC ![]() 8p1vC ![]() 8p1wC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45719.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1092 molecules ![](data/chem/img/UM6.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UM6 / #3: Chemical | ChemComp-GOL / ![]() #4: Chemical | #5: Chemical | ![]() #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 0.10 M HEPES pH 7.0, 20 % (w/v) PEG 6000, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.71→78.3 Å / Num. obs: 176313 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Rsym value: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 12 / Num. unique obs: 8792 / CC1/2: 0.75 / Rpim(I) all: 0.509 / Rrim(I) all: 1.073 / Rsym value: 0.94 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.045 Å2
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Refinement step | Cycle: 1 / Resolution: 1.71→78.3 Å
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Refine LS restraints |
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