+Open data
-Basic information
Entry | Database: PDB / ID: 5n3v | |||||||||
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Title | Thermolysin in complex with inhibitor JC292 | |||||||||
Components | Thermolysin | |||||||||
Keywords | HYDROLASE / Inhibitor / Phosphonamidate / Protease | |||||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | |||||||||
Authors | Cramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n3v.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n3v.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 5n3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n3v_validation.pdf.gz | 857.4 KB | Display | wwPDB validaton report |
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Full document | 5n3v_full_validation.pdf.gz | 858.2 KB | Display | |
Data in XML | 5n3v_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5n3v_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/5n3v ftp://data.pdbj.org/pub/pdb/validation_reports/n3/5n3v | HTTPS FTP |
-Related structure data
Related structure data | 5mnrC 5n2tC 5n2xC 5n2zC 5n31C 5n34C 5n3yC 8tlnS 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 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) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 376 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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