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- PDB-6dyz: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -
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Open data
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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 | ||||||
![]() | S-methyl-5'-thioadenosine phosphorylase | ||||||
![]() | TRANSFERASE / MTAP enzyme / cancer / phosphorylase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731.5 KB | Display | ![]() |
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Full document | ![]() | 731.5 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dyuC ![]() 6dyvC ![]() 6dywC ![]() 6dyyC ![]() 6dz0C ![]() 6dz2C ![]() 6dz3C ![]() 5tc6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 33119.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase |
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-Non-polymers , 5 types, 272 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OS2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OS2.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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