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- PDB-8r5t: Crystal structure of NDM-1 in complex with benzobisheterocycle co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8r5t | ||||||
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Title | Crystal structure of NDM-1 in complex with benzobisheterocycle compound 14. | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
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Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hinchliffe, P. / Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes. Authors: Villamil, V. / Rossi, M.A. / Mojica, M.F. / Hinchliffe, P. / Martinez, V. / Castillo, V. / Saiz, C. / Banchio, C. / Macias, M.A. / Spencer, J. / Bonomo, R.A. / Vila, A. / Moreno, D.M. / Mahler, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.9 KB | Display | ![]() |
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PDB format | ![]() | 214.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8r5uC C: citing same article ( |
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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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1 |
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2 |
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Unit cell |
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Components
#1: Protein | Mass: 25775.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-Y4E / [( | Mass: 224.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2S2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-ZN / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() 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: 36.83 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.58→35.05 Å / Num. obs: 55898 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.58→1.61 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2738 / CC1/2: 0.668 / Rpim(I) all: 0.586 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 max: 110.42 Å2 / Biso mean: 28.6065 Å2 / Biso min: 12.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→34.356 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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