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Yorodumi- PDB-8p4h: Crystal structure of human methionine adenosyltransferase 2A (MAT... -
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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 | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE / METHIONINE ADENOSYLTRANSFERASE / SAM / ALLOSTERIC INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Thomsen, M. / Thieulin-Pardo, G. / Neumann, L. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p4h.cif.gz | 627.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p4h.ent.gz | 513.5 KB | Display | PDB format |
PDBx/mmJSON format | 8p4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/8p4h ftp://data.pdbj.org/pub/pdb/validation_reports/p4/8p4h | HTTPS FTP |
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-Related structure data
Related structure data | 8p1tC 8p1vC 8p1wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase |
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-Non-polymers , 6 types, 1092 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→78.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.915 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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