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Yorodumi- PDB-7yhd: Crystal structure of VIM-2 MBL in complex with 3-(4-(4-(2-aminoet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yhd | ||||||||||||
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Title | Crystal structure of VIM-2 MBL in complex with 3-(4-(4-(2-aminoethoxy)phenyl)-1H-1,2,3-triazol-1-yl)phthalic acid | ||||||||||||
Components | Beta-lactamase class B VIM-2 | ||||||||||||
Keywords | HYDROLASE/INHIBITOR / Metallo-beta-lactamase VIM-2 / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.696 Å | ||||||||||||
Authors | Li, G.-B. / Yan, Y.-H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Metal binding pharmacophore click-derived discovery of new broad-spectrum metallo-beta-lactamase inhibitors. Authors: Yan, Y.H. / Ding, H.S. / Zhu, K.R. / Mu, B.S. / Zheng, Y. / Huang, M.Y. / Zhou, C. / Li, W.F. / Wang, Z. / Wu, Y. / Li, G.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yhd.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yhd.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yhd_validation.pdf.gz | 665.4 KB | Display | wwPDB validaton report |
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Full document | 7yhd_full_validation.pdf.gz | 673.9 KB | Display | |
Data in XML | 7yhd_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 7yhd_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/7yhd ftp://data.pdbj.org/pub/pdb/validation_reports/yh/7yhd | HTTPS FTP |
-Related structure data
Related structure data | 7yh9C 7yhaC 7yhbC 7yhcC 6jn6S S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 24679.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Pseudomonas aeruginosa / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IU7 / | #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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: May 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.696→19.392 Å / Num. obs: 22860 / % possible obs: 98.12 % / Redundancy: 11.6 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.851 / Num. unique obs: 1854 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JN6 Resolution: 1.696→19.392 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 40.93 / 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: 117.52 Å2 / Biso mean: 32.2407 Å2 / Biso min: 8.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.696→19.392 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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