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Open data
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Basic information
Entry | Database: PDB / ID: 3g2y | |||||||||
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Title | CTX-M-9 class A beta-lactamase complexed with compound 1 (GF4) | |||||||||
![]() | Beta-lactamase CTX-M-9a | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / CTX-M / beta-lactamase / molecular docking / fragment / inhibitor / Antibiotic resistance / Hydrolase / Plasmid / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, Y. / Shoichet, B.K. | |||||||||
![]() | ![]() Title: Molecular docking and ligand specificity in fragment-based inhibitor discovery Authors: Chen, Y. / Shoichet, B.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.6 KB | Display | ![]() |
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PDB format | ![]() | 182.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.1 KB | Display | ![]() |
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Full document | ![]() | 471.6 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g2zC ![]() 3g30C ![]() 3g31C ![]() 3g32C ![]() 3g34C ![]() 3g35C ![]() 1yljS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 27955.463 Da / Num. of mol.: 2 / Fragment: sequence database residues 29-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Apr 11, 2008 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→50 Å / Num. obs: 96638 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.056 / Χ2: 1.025 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YLJ Resolution: 1.31→23.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.898 / SU B: 1.629 / SU ML: 0.032 / SU R Cruickshank DPI: 0.068 / SU Rfree: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.74 Å2 / Biso mean: 13.034 Å2 / Biso min: 2.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→23.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.345 Å / Total num. of bins used: 20
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