[English] 日本語
Yorodumi- PDB-7rwh: Crystal structure of human methionine adenosyltransferase 2A (MAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rwh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-41998 | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE/INHIBITOR / METHIONINE ADENOSYLTRANSFERASE / SAM / ALLOSTERIC INHIBITOR / TRANSFERASE / 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: 1.17 Å | ||||||
Authors | Jin, L. / Padyana, A.K. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 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: Journal: J.MED.CHEM. / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rwh.cif.gz | 325.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rwh.ent.gz | 217.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rwh ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rwh | HTTPS FTP |
---|
-Related structure data
Related structure data | 7rw5C 7rw7C 7rwgC 2p02S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-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.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase |
---|
-Non-polymers , 8 types, 542 molecules
#2: Chemical | ChemComp-SAM / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-7UI / | ||||||||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-1PE / | #7: Chemical | ChemComp-CL / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→36.63 Å / Num. obs: 116890 / % possible obs: 92.3 % / Redundancy: 11.6 % / Biso Wilson estimate: 9.25 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.17→1.2 Å / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3998 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P02 Resolution: 1.17→35.95 Å / SU ML: 0.0743 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.1522 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→35.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|