[English] 日本語
![](img/lk-miru.gif)
- PDB-5n3a: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5n3a | ||||||
---|---|---|---|---|---|---|---|
Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 4-methyl-5-(1-methylimidazol-2-yl)-1,3-thiazol-2-amine | ||||||
![]() |
| ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A crystallographic fragment study with cAMP-dependent protein kinase A Authors: Siefker, C. / Heine, A. / Klebe, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5mhiC ![]() 5n1dC ![]() 5n1eC ![]() 5n1fC ![]() 5n1gC ![]() 5n1hC ![]() 5n1kC ![]() 5n1lC ![]() 5n1mC ![]() 5n1nC ![]() 5n1oC ![]() 5n32C ![]() 5n36C ![]() 5n37C ![]() 5n39C ![]() 5n3bC ![]() 5n3fC ![]() 5n3gC ![]() 5n3iC ![]() 5n3kC ![]() 5n3lC ![]() 5n3mC ![]() 5n3nC ![]() 5n3oC ![]() 5n3pC ![]() 5n3rC ![]() 5n3tC ![]() 5n7pC ![]() 4wihS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 41193.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Phosphorylation of S11, S140, T198 and S339 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 251 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/46P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/46P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-MPD / ( | ![]() #5: Chemical | ChemComp-46P / | #6: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-Solution DTT EDTA LiCl Methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2016 / Details: Silicon, active surface |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→50 Å / Num. obs: 90107 / % possible obs: 99.9 % / Redundancy: 6.62 % / CC1/2: 1 / Rrim(I) all: 0.033 / Net I/σ(I): 28.34 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 6.42 % / Mean I/σ(I) obs: 3.37 / Num. unique obs: 14385 / CC1/2: 0.89 / Rrim(I) all: 0.522 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4WIH Resolution: 1.404→39.71 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.404→39.71 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|