[English] 日本語
![](img/lk-miru.gif)
- PDB-6m8a: Crystal structure of the core catalytic domain of human inositol ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6m8a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with luteolin | ||||||
![]() | Inositol polyphosphate multikinase,Inositol polyphosphate multikinase | ||||||
![]() | TRANSFERASE/TRANSFERASE Inhibitor / kinase / inositol / inositol polyphosphate / TRANSFERASE / luteolin / flavonoid / inhibitor / natural product / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | ![]() Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity ...Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / phosphorylation / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Shears, S.B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure-Activity Analysis. Authors: Gu, C. / Stashko, M.A. / Puhl-Rubio, A.C. / Chakraborty, M. / Chakraborty, A. / Frye, S.V. / Pearce, K.H. / Wang, X. / Shears, S.B. / Wang, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 709.8 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m88C ![]() 6m89C ![]() 6m8bC ![]() 6m8cC ![]() 6m8dC ![]() 6m8eC ![]() 5w2gS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29827.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8NFU5, inositol-polyphosphate multikinase |
---|---|
#2: Chemical | ChemComp-LU2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 43.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 2 mM luteolin for 3 days. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 27243 / % possible obs: 99.9 % / Redundancy: 16 % / Biso Wilson estimate: 16.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.025 / Rrim(I) all: 0.102 / Χ2: 1.236 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 1346 / CC1/2: 0.849 / Rpim(I) all: 0.234 / Rrim(I) all: 0.909 / Χ2: 0.797 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5w2g Resolution: 1.75→36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.448 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.123 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.036 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|