[English] 日本語
![](img/lk-miru.gif)
- PDB-6yms: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yms | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / Phosphoramidate Inhibitor / Protease | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kljajic, M. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin Authors: Kljajic, M. / Gerber, H.-D. / Heine, A. / Klebe, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 249 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 167.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6y4iC ![]() 6yi6C ![]() 6ymrC ![]() 5lvdS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nprS, nprM / Production host: ![]() ![]() |
---|
-Non-polymers , 7 types, 373 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/OZH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/OZH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | ChemComp-OZH / ( | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M CsCl, 50 mM Tris(hydroxymethyl)aminomethane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→46.31 Å / Num. obs: 76712 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/σ(I): 19.89 |
Reflection shell | Resolution: 1.32→1.4 Å / Mean I/σ(I) obs: 4.55 / Num. unique obs: 12067 / CC1/2: 0.94 / Rrim(I) all: 0.516 / Rsym value: 0.495 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5LVD Resolution: 1.32→46.31 Å / SU ML: 0.0813 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3655
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→46.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|