+Open data
-Basic information
Entry | Database: PDB / ID: 8xam | ||||||
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Title | Co-crystal structure of compound 7 in complex with MAT2A | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE / MAT2A inhibitor | ||||||
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: 1.3 Å | ||||||
Authors | Gao, F. / Ding, X. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2024 Title: Discovery of novel MAT2A inhibitors by an allosteric site-compatible fragment growing approach. Authors: Gao, F. / Ding, X. / Cao, Z. / Zhu, W. / Fan, Y. / Steurer, B. / Wang, H. / Cai, X. / Zhang, M. / Aliper, A. / Ren, F. / Ding, X. / Zhavoronkov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xam.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xam.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/8xam ftp://data.pdbj.org/pub/pdb/validation_reports/xa/8xam | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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
#1: Protein | Mass: 42001.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia phage EcWhh-1 (virus) / References: UniProt: P31153, methionine adenosyltransferase #2: Chemical | #3: Chemical | ChemComp-XRH / | Mass: 670.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H29Cl2N7O4 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | 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: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.2 M LiCl, 0.1 M Tris pH 8.0, (18%-20%) PEG6000, 10% Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 1.1807 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1807 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→47.02 Å / Num. obs: 169065 / % possible obs: 94.1 % / Redundancy: 6.9 % / CC1/2: 1 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.3→1.32 Å / Num. unique obs: 7991 / CC1/2: 0.931 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40.119 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.529 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.041 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: 11.625 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→40.119 Å
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Refine LS restraints |
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LS refinement shell |
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