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Yorodumi- PDB-6dyz: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dyz | ||||||
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Title | Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((prop-2-yn-1-ylthio)methyl)pyrrolidin-3-ol | ||||||
Components | S-methyl-5'-thioadenosine phosphorylase | ||||||
Keywords | TRANSFERASE / MTAP enzyme / cancer / phosphorylase | ||||||
Function / homology | Function and homology information Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Harijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2019 Title: Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase. Authors: Harijan, R.K. / Hoff, O. / Ducati, R.G. / Firestone, R.S. / Hirsch, B.M. / Evans, G.B. / Schramm, V.L. / Tyler, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dyz.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dyz.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dyz ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dyz | HTTPS FTP |
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-Related structure data
Related structure data | 6dyuC 6dyvC 6dywC 6dyyC 6dz0C 6dz2C 6dz3C 5tc6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 33119.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTAP, MSAP / Production host: Escherichia coli (E. coli) References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase |
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-Non-polymers , 5 types, 272 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Chemical | ChemComp-OS2 / ( | #6: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 58.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, pH 7.0, 10% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 14, 2017 / Details: KB mirrors |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→106.37 Å / Num. obs: 48526 / % possible obs: 98.6 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 2 |
Reflection shell | Resolution: 1.62→1.65 Å / Num. measured obs: 28477 / CC1/2: 0.758 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TC6 Resolution: 1.62→106.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.629 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.065 Å2
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Refinement step | Cycle: 1 / Resolution: 1.62→106.37 Å
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Refine LS restraints |
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