[English] 日本語
![](img/lk-miru.gif)
- PDB-8hxn: Crystal structure of B2 Sfh-I MBL in complex with 2-amino-5-(4-(b... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8hxn | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of B2 Sfh-I MBL in complex with 2-amino-5-(4-(but-3-en-1-yloxy)benzyl)thiazole-4-carboxylic acid | ||||||||||||
![]() | Beta-lactamase | ||||||||||||
![]() | HYDROLASE / Beta-lactamase class B Sfh-I | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yan, Y.-H. / Zhu, K.-R. / Li, G.-B. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. Authors: Yan, Y.H. / Zhang, T.T. / Li, R. / Wang, S.Y. / Wei, L.L. / Wang, X.Y. / Zhu, K.R. / Li, S.R. / Liang, G.Q. / Yang, Z.B. / Yang, L.L. / Qin, S. / Li, G.B. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 794 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hx5C ![]() 8hxeC ![]() 8hxiC ![]() 8hxoC ![]() 8hxpC ![]() 8hxuC ![]() 8hxvC ![]() 8hxwC ![]() 8hy1C ![]() 8hy2C ![]() 8hy6C ![]() 8hydC ![]() 8jaoC ![]() 5ew0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25947.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-5I6 / |
#4: Chemical | ChemComp-EOH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.35 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-40 mM Ammonium nitrate, 1% Isopropyl alcohol, 30% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Oct 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→36.93 Å / Num. obs: 46148 / % possible obs: 99.7 % / Redundancy: 12.4 % / CC1/2: 1 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.35→1.42 Å / Num. unique obs: 6530 / CC1/2: 0.815 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5EW0 Resolution: 1.35→36.93 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.96 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→36.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|