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Yorodumi- PDB-8r5t: Crystal structure of NDM-1 in complex with benzobisheterocycle co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r5t | ||||||
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Title | Crystal structure of NDM-1 in complex with benzobisheterocycle compound 14. | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / metallo-beta-lactamase / inhibitor | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.58 Å | ||||||
Authors | Hinchliffe, P. / Spencer, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r5t.cif.gz | 262.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r5t.ent.gz | 214.3 KB | Display | PDB format |
PDBx/mmJSON format | 8r5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r5t_validation.pdf.gz | 779.3 KB | Display | wwPDB validaton report |
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Full document | 8r5t_full_validation.pdf.gz | 781.5 KB | Display | |
Data in XML | 8r5t_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 8r5t_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/8r5t ftp://data.pdbj.org/pub/pdb/validation_reports/r5/8r5t | HTTPS FTP |
-Related structure data
Related structure data | 8r5uC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.87 Å |
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: 0.87 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→34.356 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.1 / Stereochemistry target values: ML
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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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