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Yorodumi- PDB-5zfi: Mouse kallikrein 7 in complex with 6-benzyl-1,4-diazepan-7-one de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfi | ||||||
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Title | Mouse kallikrein 7 in complex with 6-benzyl-1,4-diazepan-7-one derivative | ||||||
Components | Kallikrein-7 | ||||||
Keywords | HYDROLASE / protease / inhibitor complex | ||||||
Function / homology | Function and homology information stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / Degradation of the extracellular matrix / cornified envelope / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sugawara, H. | ||||||
Citation | Journal: Bioorg. Med. Chem. / Year: 2018 Title: Structure-based drug design to overcome species differences in kallikrein 7 inhibition of 1,3,6-trisubstituted 1,4-diazepan-7-ones. Authors: Murafuji, H. / Sugawara, H. / Goto, M. / Oyama, Y. / Sakai, H. / Imajo, S. / Tomoo, T. / Muto, T. #1: Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors. Authors: Murafuji, H. / Sakai, H. / Goto, M. / Imajo, S. / Sugawara, H. / Muto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zfi.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfi.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 5zfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zfi_validation.pdf.gz | 747.5 KB | Display | wwPDB validaton report |
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Full document | 5zfi_full_validation.pdf.gz | 749.3 KB | Display | |
Data in XML | 5zfi_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5zfi_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfi ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfi | HTTPS FTP |
-Related structure data
Related structure data | 5zfhSC 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
#1: Protein | Mass: 24637.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klk7, Prss6, Scce / Production host: Escherichia coli (E. coli) References: UniProt: Q91VE3, stratum corneum chymotryptic enzyme |
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#2: Chemical | ChemComp-9C9 / |
#3: Chemical | ChemComp-TRS / |
#4: 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: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG400, PEG 8000, magnesium chloride, Tris/HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 22651 / % possible obs: 95.1 % / Redundancy: 9.6 % / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.284 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZFH Resolution: 1.8→30.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.446 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.856 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→30.15 Å
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Refine LS restraints |
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