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- PDB-6b1w: Crystal structure KPC-2 beta-lactamase complexed with WCK 5107 by... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b1w | ||||||
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Title | Crystal structure KPC-2 beta-lactamase complexed with WCK 5107 by co-crystallization | ||||||
![]() | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
![]() | HYDROLASE/HYDROLASE Inhibitor / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Akker, F. / Nguyen, N.Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234. Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961.2 KB | Display | ![]() |
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Full document | ![]() | 964.4 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b1fC ![]() 6b1hC ![]() 6b1jC ![]() 6b1xC ![]() 6b1yC ![]() 6b22C C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28348.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 200mM Lithium sulfate, 100mM sodium acetate pH 4.4-4.6, and 28-31% PEG8000. Protein to inhibitor molar ratio of 1 is to 10 and KPC-2 concentration was 10 mg/mL. PH range: 4.4 - 4.6 / Temp details: RT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12708 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→37.13 Å / Num. obs: 40430 / % possible obs: 95.3 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Net I/σ(I): 12.8 / Num. measured all: 80088 / Scaling rejects: 0 |
Reflection shell | Resolution: 1.73→1.77 Å / Redundancy: 2 % / Rmerge(I) obs: 0.345 / Num. unique obs: 2129 / CC1/2: 0.716 / Rpim(I) all: 0.345 / Rrim(I) all: 0.487 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.77 Å2 / Biso mean: 14.04 Å2 / Biso min: 5.9 Å2
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Refinement step | Cycle: final / Resolution: 1.73→34.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.732→1.777 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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