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Yorodumi- PDB-2q9m: 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q9m | ||||||
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Title | 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase inhibitor / tricyclic carbapenem | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Plantan, I. / Selic, L. / Mesar, T. / Stefanic Anderluh, P. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. ...Plantan, I. / Selic, L. / Mesar, T. / Stefanic Anderluh, P. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / Copar, A. / Urleb, U. / Solmajer, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: 4-Substituted Trinems as Broad Spectrum beta-Lactamase Inhibitors: Structure-Based Design, Synthesis, and Biological Activity Authors: Plantan, I. / Selic, L. / Mesar, T. / Anderluh, P.S. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / ...Authors: Plantan, I. / Selic, L. / Mesar, T. / Anderluh, P.S. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / Copar, A. / Urleb, U. / Solmajer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q9m.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q9m.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 2q9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q9m_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 2q9m_full_validation.pdf.gz | 817.6 KB | Display | |
Data in XML | 2q9m_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2q9m_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/2q9m ftp://data.pdbj.org/pub/pdb/validation_reports/q9/2q9m | HTTPS FTP |
-Related structure data
Related structure data | 2q9nC 1xx2S 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: 39040.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacter cloacae (bacteria) / Strain: 908R / References: UniProt: P05364, beta-lactamase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05M Cacodylate, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2001 |
Radiation | Monochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 21206 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.05→2.09 Å / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XX2 Resolution: 2.05→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.09 Å / % reflection obs: 84.9 % |