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Yorodumi- PDB-8qdz: Crystal structure of human MAT2a bound to S-Adenosylmethionine an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qdz | ||||||
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Title | Crystal structure of human MAT2a bound to S-Adenosylmethionine and Compound 11 | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE / S-Adenosylmethionine biosynthesis / allosteric 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: 1.16 Å | ||||||
Authors | Schimpl, M. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Development of a Series of Pyrrolopyridone MAT2A Inhibitors. Authors: Atkinson, S.J. / Bagal, S.K. / Argyrou, A. / Askin, S. / Cheung, T. / Chiarparin, E. / Coen, M. / Collie, I.T. / Dale, I.L. / De Fusco, C. / Dillman, K. / Evans, L. / Feron, L.J. / Foster, A. ...Authors: Atkinson, S.J. / Bagal, S.K. / Argyrou, A. / Askin, S. / Cheung, T. / Chiarparin, E. / Coen, M. / Collie, I.T. / Dale, I.L. / De Fusco, C. / Dillman, K. / Evans, L. / Feron, L.J. / Foster, A.J. / Grondine, M. / Kantae, V. / Lamont, G.M. / Lamont, S. / Lynch, J.T. / Nilsson Lill, S. / Robb, G.R. / Saeh, J. / Schimpl, M. / Scott, J.S. / Smith, J. / Srinivasan, B. / Tentarelli, S. / Vazquez-Chantada, M. / Wagner, D. / Walsh, J.J. / Watson, D. / Williamson, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qdz.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qdz.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 8qdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/8qdz ftp://data.pdbj.org/pub/pdb/validation_reports/qd/8qdz | HTTPS FTP |
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-Related structure data
Related structure data | 8qdyC 8qe0C 8qe1C 8qe2C 8qe3C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43935.828 Da / Num. of mol.: 1 / Fragment: full length protein 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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#2: Chemical | ChemComp-U6R / Mass: 281.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O2 / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-SAM / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 8-12 % PEG 8000, 8-12 % ethylene glycol, 0.1 M Hepes pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→58.62 Å / Num. obs: 88119 / % possible obs: 93.2 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.16→1.251 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4405 / CC1/2: 0.535 / % possible all: 60.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→58.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.964 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.049 / SU Rfree Blow DPI: 0.048 / SU Rfree Cruickshank DPI: 0.047
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Displacement parameters | Biso mean: 15.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→58.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.21 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 25.7985 Å / Origin y: 38.8789 Å / Origin z: 32.3824 Å
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Refinement TLS group | Selection details: { A|* } |