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Open data
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Basic information
Entry | Database: PDB / ID: 5n3v | |||||||||
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Title | Thermolysin in complex with inhibitor JC292 | |||||||||
![]() | 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 | ![]() | 205.2 KB | Display | ![]() |
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PDB format | ![]() | 165.6 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 ![]() 5n2tC ![]() 5n2xC ![]() 5n2zC ![]() 5n31C ![]() 5n34C ![]() 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 , 6 types, 376 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/8L5.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/8L5.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-8L5 / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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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: Oct 25, 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: 1.12→50 Å / Num. obs: 125558 / % possible obs: 99.4 % / Redundancy: 5.49 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.1 / Net I/σ(I): 11.47 |
Reflection shell | Resolution: 1.12→1.189 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 19848 / CC1/2: 0.88 / Rrim(I) all: 0.49 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8TLN Resolution: 1.12→40.138 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 8.16 / 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: 1.12→40.138 Å
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Refine LS restraints |
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LS refinement shell |
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