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Open data
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Basic information
Entry | Database: PDB / ID: 4n4e | ||||||
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Title | Thermolysin in complex with UBTLN58 | ||||||
![]() | Thermolysin | ||||||
![]() | hydrolase/hydrolase inhibitor / Protease / Metalloprotease / Hydrolysis of peptide bonds / 2-Phosphoramidon / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors. Authors: Krimmer, S.G. / Betz, M. / 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 | ![]() | 163.6 KB | Display | ![]() |
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PDB format | ![]() | 127.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 948.3 KB | Display | ![]() |
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Full document | ![]() | 949.7 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mtwC ![]() 4mwpC ![]() 4mxjC ![]() 4mznC ![]() 4n5pC ![]() 4n66C ![]() 4oi5C ![]() 8tlnS 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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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 / Fragment: Mature form (UNP residues 233-548) / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 474 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/2G6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/2G6.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-2G6 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM Tris/HCl, 1.9 M CsCl, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 / Details: Mirror |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→50 Å / Num. obs: 118776 / % possible obs: 95.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 8.297 Å2 / Rsym value: 0.064 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.13→1.15 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 6.31 / Num. unique all: 4789 / Rsym value: 0.282 / % possible all: 78.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 8TLN Resolution: 1.13→31.814 Å / SU ML: 0.07 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 11.5 / 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: 1.13→31.814 Å
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Refine LS restraints |
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LS refinement shell |
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