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Open data
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Basic information
Entry | Database: PDB / ID: 4exs | ||||||
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Title | Crystal structure of NDM-1 bound to L-captopril | ||||||
![]() | Beta-lactamase NDM-1 | ||||||
![]() | Hydrolase/antibiotic / Metallo-Beta-Lactamase / antibiotic / Hydrolase-antibiotic complex | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Strynadka, N.C.J. / King, D.T. | ||||||
![]() | ![]() Title: New Delhi Metallo-Beta-Lactamase: Structural Insights into Beta-Lactam Recognition and Inhibition Authors: King, D.T. / Worrall, L.J. / Gruninger, R. / Strynadka, N.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.1 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4exyC ![]() 4ey2C ![]() 4eybC ![]() 4eyfC ![]() 4eylC ![]() 3q6x 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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Details | Biologically active form may be a dimer or monomer |
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Components
#1: Protein | Mass: 28739.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10%w/v peg 8K, 8%v/v ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 22, 2011 |
Radiation | Monochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→58.71 Å / Num. all: 24492 / Num. obs: 21474 / % possible obs: 99 % / Observed criterion σ(I): -3 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.59 Å / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6X ![]() 3q6x Resolution: 2.4→58.71 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.849 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.252 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.252 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→58.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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