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- PDB-8b20: NDM-1 metallo-beta-lactamase in complex with triazole-based inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b20 | ||||||
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Title | NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP57 | ||||||
![]() | Beta-lactamase NDM-1 | ||||||
![]() | HYDROLASE / Beta-lactamase / Antibiotic resistance / Beta-lactamase inhibitor | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / antibiotic catabolic process / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase / hydrolase activity / Chem-OQK / Metallo-beta-lactamase type 2![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vascon, F. / Lazzarato, L. / Bersani, M. / Gianquinto, E. / Docquier, J.D. / Spyrakis, F. / Tondi, D. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-beta-Lactamases and Synergistic Activity on Resistant Bacteria. Authors: Bersani, M. / Failla, M. / Vascon, F. / Gianquinto, E. / Bertarini, L. / Baroni, M. / Cruciani, G. / Verdirosa, F. / Sannio, F. / Docquier, J.D. / Cendron, L. / Spyrakis, F. / Lazzarato, 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 | ![]() | 106 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 794.1 KB | Display | ![]() |
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Full document | ![]() | 797.6 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b1wC ![]() 8b1zC ![]() 6tgdS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 146 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OQK.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OQK.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-OQK / | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 hexahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→53.31 Å / Num. obs: 39230 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 7 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2195 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TGD Resolution: 1.78→53.306 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.117 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→53.306 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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