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Open data
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Basic information
Entry | Database: PDB / ID: 5n2t | ||||||
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Title | Thermolysin in complex with inhibitor JC287 | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / Inhibitor / Phosphonamidate / Protease | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors. Authors: Cramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.4 KB | Display | ![]() |
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PDB format | ![]() | 164.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mnrC ![]() 5n2xC ![]() 5n2zC ![]() 5n31C ![]() 5n34C ![]() 5n3vC ![]() 5n3yC ![]() 8tlnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 378 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/8KK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/8KK.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-8KK / ~{ | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4 mM TLN, 1.9 M CsCl, 50% DMSO, 50 mM Tris-HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.379→50 Å / Num. obs: 69141 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 28.36 |
Reflection shell | Resolution: 1.379→1.459 Å / Redundancy: 12 % / Rmerge(I) obs: 0.49 / Num. unique obs: 10972 / CC1/2: 0.942 / Rsym value: 0.51 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8TLN Resolution: 1.379→46.523 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.37 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.379→46.523 Å
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Refine LS restraints |
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LS refinement shell |
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