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Yorodumi- PDB-6l40: Discovery of novel peptidomimetic boronate ClpP inhibitors with n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l40 | ||||||
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Title | Discovery of novel peptidomimetic boronate ClpP inhibitors with noncanonical enzyme mechanism as potent virulence blockers in vitro and in vivo | ||||||
Components | ATP-dependent Clp protease proteolytic subunit | ||||||
Keywords | HYDROLASE/INHIBITOR / Caseinolytic protease P (ClpP) / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.209 Å | ||||||
Authors | Luo, Y.F. / Bao, R. / Ju, Y. / He, L.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockersin Vitroandin Vivo. Authors: Ju, Y. / He, L. / Zhou, Y. / Yang, T. / Sun, K. / Song, R. / Yang, Y. / Li, C. / Sang, Z. / Bao, R. / Luo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l40.cif.gz | 483.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l40.ent.gz | 400.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l40_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 6l40_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 6l40_validation.xml.gz | 96.8 KB | Display | |
Data in CIF | 6l40_validation.cif.gz | 122.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l40 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l40 | HTTPS FTP |
-Related structure data
Related structure data | 6l3xC 5c90S S: Starting model for refinement C: citing same article (ref.) |
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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: 19243.889 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / Gene: clpP, SAB0722 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YSF8, endopeptidase Clp #2: Chemical | ChemComp-FN3 / [( #3: 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: 3.3 Å3/Da / Density % sol: 62.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium chloride, 0.1M HEPES pH 7.5 and 1.6 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2088→24.3026 Å / Num. obs: 171585 / % possible obs: 99.71 % / Redundancy: 9.6 % / Biso Wilson estimate: 36.64 Å2 / Rpim(I) all: 0.072 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.3→2.3621 Å / Num. unique obs: 14 / CC1/2: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C90 Resolution: 2.209→24.301 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.74 / 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: 105.99 Å2 / Biso mean: 44.2651 Å2 / Biso min: 19.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.209→24.301 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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