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Yorodumi- PDB-1mmj: Porcine pancreatic elastase complexed with a potent peptidyl inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mmj | ||||||
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Title | Porcine pancreatic elastase complexed with a potent peptidyl inhibitor, FR136706 | ||||||
Components | elastase 1 | ||||||
Keywords | HYDROLASE / chymotrypsin family | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kinoshita, T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: True interaction mode of porcine pancreatic elastase with FR136706, a potent peptidyl inhibitor Authors: Kinoshita, T. / Nakanishi, I. / Sato, A. / Tada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmj.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmj.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mmj_validation.pdf.gz | 641 KB | Display | wwPDB validaton report |
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Full document | 1mmj_full_validation.pdf.gz | 671.6 KB | Display | |
Data in XML | 1mmj_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1mmj_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmj ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: pancreatic / References: UniProt: P00772, pancreatic elastase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-FR1 / |
#5: 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: 2.18 Å3/Da / Density % sol: 43.5 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium sulphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: Sawyer, L., (1978) J. Mol. Biol., 118, 137 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.7107 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 11, 1999 / Details: monochrometer |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 15865 / Num. obs: 15865 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 |
Reflection shell | Resolution: 2.2→2.35 Å / % possible all: 90.9 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 90.9 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.227 |