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- PDB-6lj5: Crystal structure of NDM-1 in complex with D-captopril derivative... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lj5 | ||||||
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Title | Crystal structure of NDM-1 in complex with D-captopril derivative wss04145 | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds / ANTIBIOTIC | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, H. / Ma, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors. Authors: Ma, G. / Wang, S. / Wu, K. / Zhang, W. / Ahmad, A. / Hao, Q. / Lei, X. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.5 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.9 KB | Display | ![]() |
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Full document | ![]() | 770 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lipC ![]() 6lizC ![]() 6lj0C ![]() 6lj1C ![]() 6lj2C ![]() 6lj4C ![]() 6lj6C ![]() 6lj7C ![]() 6lj8C ![]() 5xp6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | ChemComp-EF0 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.93 % / Mosaicity: 0.569 ° / Mosaicity esd: 0.005 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→50 Å / Num. obs: 53699 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 1.48 / Net I/σ(I): 12 / Num. measured all: 352156 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XP6 Resolution: 1.26→24.39 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.73 Å2 / Biso mean: 23.6045 Å2 / Biso min: 8.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.26→24.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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