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- PDB-7rwg: "Crystal structure of human methionine adenosyltransferase 2A (MA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rwg | ||||||
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Title | "Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-43192 | ||||||
![]() | S-adenosylmethionine synthase isoform type-2 | ||||||
![]() | TRANSFERASE/INHIBITOR / METHIONINE ADENOSYLTRANSFERASE / SAM / ALLOSTERIC INHIBITOR / TRANSFERASE / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | ![]() methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / cellular response to methionine / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / positive regulation of TORC1 signaling ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / cellular response to methionine / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, L. / Padyana, A.K. | ||||||
Funding support | 1items
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![]() | ![]() Title: Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads. Authors: Li, M. / Konteatis, Z. / Nagaraja, N. / Chen, Y. / Zhou, S. / Ma, G. / Gross, S. / Marjon, K. / Hyer, M.L. / Mandley, E. / Lein, M. / Padyana, A.K. / Jin, L. / Tong, S. / Peters, R. / ...Authors: Li, M. / Konteatis, Z. / Nagaraja, N. / Chen, Y. / Zhou, S. / Ma, G. / Gross, S. / Marjon, K. / Hyer, M.L. / Mandley, E. / Lein, M. / Padyana, A.K. / Jin, L. / Tong, S. / Peters, R. / Murtie, J. / Travins, J. / Medeiros, M. / Liu, P. / Frank, V. / Judd, E.T. / Biller, S.A. / Marks, K.M. / Sui, Z. / Reznik, S.K. #1: ![]() Title: DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR Authors: Konteatis, Z. / Travins, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.2 KB | Display | ![]() |
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PDB format | ![]() | 218.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rw5C ![]() 7rw7C ![]() 7rwhC ![]() 2p02S C: citing same article ( S: Starting model for refinement |
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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 A
#1: Protein | Mass: 43807.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 619 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/7UN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/7UN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAM / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-7UN / ( | #6: Chemical | ChemComp-GOL / | #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: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→46.86 Å / Num. obs: 207397 / % possible obs: 95.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 6.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 0.97→0.99 Å / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9856 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2P02 Resolution: 0.97→39.95 Å / SU ML: 0.0951 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.0123 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→39.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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