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- PDB-6tma: VIM-2_1dj- Triazole inhibitors with promising inhibitor effects a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tma | ||||||
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Title | VIM-2_1dj- Triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases | ||||||
![]() | Beta-lactamase class B VIM-2 | ||||||
![]() | ANTIBIOTIC / Metallo-beta-lactamase inhibitor / NH-triazole / inhibition properties / crystal structure. | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leiros, H.-K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural studies of triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases. Authors: Muhammad, Z. / Skagseth, S. / Boomgaren, M. / Akhter, S. / Frohlich, C. / Ismael, A. / Christopeit, T. / Bayer, A. / Leiros, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.2 KB | Display | ![]() |
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PDB format | ![]() | 235.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tm9C ![]() 6tmbC ![]() 6tmcC ![]() 5lscS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28352.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Production host: ![]() ![]() |
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-Non-polymers , 6 types, 643 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/9O8.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/9O8.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #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: 1.83 Å3/Da / Density % sol: 32.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: 22-27% PEG 3350 and 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983998 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.63 Å / Num. obs: 64863 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.39 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.5→1.52 Å / Rmerge(I) obs: 0.879 / Num. unique obs: 2749 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LSC Resolution: 1.5→39.63 Å / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8128 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.63 Å
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Refine LS restraints |
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LS refinement shell |
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