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- PDB-6lip: 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: 6lip | ||||||
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Title | Crystal structure of NDM-1 in complex with D-captopril derivative wss0218 | ||||||
![]() | 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 | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.5 KB | Display | ![]() |
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Full document | ![]() | 842.2 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lizC ![]() 6lj0C ![]() 6lj1C ![]() 6lj2C ![]() 6lj4C ![]() 6lj5C ![]() 6lj6C ![]() 6lj7C ![]() 6lj8C ![]() 5xp6S 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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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 | #3: Chemical | ChemComp-EEL / ( | #4: 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: 39.87 % / Mosaicity: 0.261 ° / Mosaicity esd: 0.003 ° |
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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: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.98→50 Å / Num. obs: 113420 / % possible obs: 96 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Χ2: 0.844 / Net I/σ(I): 14.1 / Num. measured all: 819276 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XP6 Resolution: 0.98→27.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.557 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.09 Å2 / Biso mean: 20.823 Å2 / Biso min: 12.97 Å2
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Refinement step | Cycle: final / Resolution: 0.98→27.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1.005 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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