[English] 日本語
![](img/lk-miru.gif)
- PDB-6dz3: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6dz3 | ||||||
---|---|---|---|---|---|---|---|
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-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol | ||||||
![]() | S-methyl-5'-thioadenosine phosphorylase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / MTAP enzyme / cancer / phosphorylase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dyuC ![]() 6dyvC ![]() 6dywC ![]() 6dyyC ![]() 6dyzC ![]() 6dz0C ![]() 6dz2C ![]() 5tc6S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 9 - 281 / Label seq-ID: 23 - 295
NCS ensembles :
|
-
Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 33119.051 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase |
---|
-Non-polymers , 5 types, 354 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OS6.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OS6.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-ACY / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.61 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100 mM sodium acetate trihydrate, pH 4.6, 2.0 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 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: 1.91→79.43 Å / Num. obs: 66387 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.99 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4430 / CC1/2: 0.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 5TC6 Resolution: 1.91→79.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.869 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.196 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.91→79.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|