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Open data
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Basic information
Entry | Database: PDB / ID: 8sqf | ||||||
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Title | OXA-48 bound to inhibitor CDD-2725 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE/INHIBITOR / carbapenemase / beta-lactamase / small molecule / 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. / Prasad, B.V.V. / Palzkill, T. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.4 KB | Display | ![]() |
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PDB format | ![]() | 91 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sqgC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.83 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.8 Å / Num. obs: 56843 / % possible obs: 87.2 % / Redundancy: 16 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.43 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7479 / CC1/2: 0.976 / % possible all: 80.4 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.8 Å
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Refine LS restraints |
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LS refinement shell |
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