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- PDB-4k8y: Atomic resolution crystal structures of Kallikrein-Related Peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k8y | ||||||
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Title | Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with Sunflower Trypsin Inhibitor (SFTI-1) | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Bowman-Birk Inhibitor / Protease / Protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding ...biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ilyichova, O.V. / Swedberg, J.E. / de Veer, S.J. / Sit, K.C. / Harris, J.M. / Buckle, A.M. | ||||||
![]() | ![]() Title: Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics Authors: Riley, B.T. / Ilyichova, O. / Costa, M.G.S. / Porebski, B.T. / de Veer, S.J. / Swedberg, J.E. / Kass, I. / Harris, J.M. / Hoke, D.E. / Buckle, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 407.8 KB | Display | ![]() |
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Full document | ![]() | 407.7 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k1eC ![]() 4kgaC ![]() 2bdgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23926.010 Da / Num. of mol.: 1 / Fragment: Related Peptidase 4, UNP residues 31-253 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/peptide | |
#3: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE IS NATURAL VARIANT (VARIANT RS2569527) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 20%(w/v) PEG 8000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2012 | ||||||||||||||||||
Radiation | Monochromator: Si(111): 4.5-21 keV, Si(311): 11-35 keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1→29.3 Å / Num. all: 100687 / Num. obs: 100687 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 6.029 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 8.7 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.9 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BDG Resolution: 1→29.296 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9167 / SU ML: 0.09 / σ(F): 1.34 / Phase error: 15.56 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.02 Å2 / Biso mean: 11.9559 Å2 / Biso min: 4.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→29.296 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36
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