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Yorodumi- PDB-6lj6: Crystal structure of NDM-1 in complex with D-captopril derivative... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lj6 | ||||||
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Title | Crystal structure of NDM-1 in complex with D-captopril derivative wss05008 | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds / ANTIBIOTIC | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Zhang, H. / Ma, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lj6.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lj6.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6lj6 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6lj6 | HTTPS FTP |
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-Related structure data
Related structure data | 6lipC 6lizC 6lj0C 6lj1C 6lj2C 6lj4C 6lj5C 6lj7C 6lj8C 5xp6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase | ||||
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#2: Chemical | ChemComp-EFF / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.09 % / Mosaicity: 0.494 ° / Mosaicity esd: 0.007 ° |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.27→50 Å / Num. obs: 53925 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Χ2: 0.939 / Net I/σ(I): 10.7 / Num. measured all: 352006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XP6 Resolution: 1.27→27.98 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.33 Å2 / Biso mean: 22.9223 Å2 / Biso min: 8.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.27→27.98 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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