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- PDB-6j8q: Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibito... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j8q | ||||||
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Title | Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 | ||||||
![]() | Serine Beta-Lactamase KPC-2 | ||||||
![]() | HYDROLASE / Beta-lactamase / Serine-beta-lactamase KPC-2 / KPC-2 / Carbapenemase | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Li, G.-B. / Liu, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases. Authors: Wang, Y.L. / Liu, S. / Yu, Z.J. / Lei, Y. / Huang, M.Y. / Yan, Y.H. / Ma, Q. / Zheng, Y. / Deng, H. / Sun, Y. / Wu, C. / Yu, Y. / Chen, Q. / Wang, Z. / Wu, Y. / Li, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.3 KB | Display | ![]() |
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PDB format | ![]() | 183.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.2 KB | Display | ![]() |
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Full document | ![]() | 511.2 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 69.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j8rC ![]() 6jn3C ![]() 6jn4C ![]() 6jn5C ![]() 6jn6C ![]() 3rxwS S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28079.584 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Klebsiella pneumoniae / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase |
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-Non-polymers , 5 types, 836 molecules ![](data/chem/img/BHU.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BHU / [[( #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-ACY / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 1, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→50 Å / Num. obs: 136404 / % possible obs: 97 % / Redundancy: 16.5 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.057 / Rrim(I) all: 0.228 / Χ2: 0.985 / Net I/σ(I): 3.1 / Num. measured all: 2249490 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RXW Resolution: 1.787→47.677 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.22 Å2 / Biso mean: 23.3258 Å2 / Biso min: 4.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.787→47.677 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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