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- PDB-6kbr: Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kbr | ||||||
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Title | Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Protein engineering / Cystine knot protein / Protease inhibitor / Structural analysis / PROTEIN BINDING / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / spermatid development / extracellular matrix disassembly / serine-type peptidase activity / acrosomal vesicle / secretory granule ...biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / spermatid development / extracellular matrix disassembly / serine-type peptidase activity / acrosomal vesicle / secretory granule / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawaguchi, Y. / Nishimiya, D. | ||||||
![]() | ![]() Title: A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases. Authors: Nishimiya, D. / Kawaguchi, Y. / Kodama, S. / Nasu, H. / Yano, H. / Yamaguchi, A. / Tamura, M. / Hashimoto, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.7 KB | Display | ![]() |
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PDB format | ![]() | 49.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bdgS 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
#1: Protein | Mass: 27048.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 7259.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Lithium chloride, polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→72.577 Å / Num. obs: 20687 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 1283 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BDG Resolution: 2→72.577 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.053 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.166 / 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: 10.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2→72.577 Å
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Refine LS restraints |
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