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- PDB-6b1f: Crystal structure KPC-2 beta-lactamase complexed with WCK 4234 by... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b1f | ||||||
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Title | Crystal structure KPC-2 beta-lactamase complexed with WCK 4234 by soaking | ||||||
![]() | 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 | ![]() | 122 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6b1hC ![]() 6b1jC ![]() 6b1wC ![]() 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 | #3: Chemical | ChemComp-CIT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20% PEG 6000, 100 mM citrate pH 4.0, 100 mM KSCN, and 10 mM CdCl2. Crystal soaked for 3hr in 10mM WCK 4234 Temp details: RT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / 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: 1.44→37.24 Å / Num. obs: 67950 / % possible obs: 91.6 % / Redundancy: 2 % / Net I/σ(I): 13.1 |
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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: 62.65 Å2 / Biso mean: 12.081 Å2 / Biso min: 4.43 Å2
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Refinement step | Cycle: final / Resolution: 1.44→31.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.441→1.478 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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