+
Open data
-
Basic information
Entry | Database: PDB / ID: 8sqg | ||||||
---|---|---|---|---|---|---|---|
Title | OXA-48 bound to inhibitor CDD-2801 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE/INHIBITOR / carbapenemase / beta-lactamase / serine protease / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, S. / Judge, A. / Fan, J. / Sankaran, B. / Palzkill, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Exploiting the Carboxylate-Binding Pocket of beta-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. Authors: Park, S. / Fan, J. / Chamakuri, S. / Palaniappan, M. / Sharma, K. / Qin, X. / Wang, J. / Tan, Z. / Judge, A. / Hu, L. / Sankaran, B. / Li, F. / Prasad, B.V.V. / Matzuk, M.M. / Palzkill, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sqfC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 30439.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OXA-48 Beta-lactamase / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.87 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% (v/v) PEG 550 MME, 0.1 M TRIS-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 16, 2022 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→33.52 Å / Num. obs: 46045 / % possible obs: 99.88 % / Redundancy: 22.7 % / Biso Wilson estimate: 27.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.08 |
Reflection shell | Resolution: 2.03→2.103 Å / Mean I/σ(I) obs: 3.35 / Num. unique obs: 4529 / CC1/2: 0.914 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→33.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|