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- PDB-5ll7: Crystal structure of KPC-2 carbapenemase in complex with a phenyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ll7 | ||||||
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Title | Crystal structure of KPC-2 carbapenemase in complex with a phenyl boronic inhibitor. | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / carbapenemase / beta-lactamase / phenyl boronic inhibitor | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vicario, M. / Celenza, G. / Bellio, P. / Perilli, M.G. / Tondi, D. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance. Authors: Celenza, G. / Vicario, M. / Bellio, P. / Linciano, P. / Perilli, M. / Oliver, A. / Blazquez, J. / Cendron, L. / Tondi, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.6 KB | Display | ![]() |
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PDB format | ![]() | 48.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mgiC ![]() 3c5aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28390.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-6YV / (~{ | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 15% polyethylene glycol 6000 (PEG 6000), 200mM potassium thiocyanate (KSCN), 100 mM sodium citrate (pH 4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40.565 Å / Num. obs: 46694 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3C5A Resolution: 1.4→40.565 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.4→40.565 Å
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