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Yorodumi- PDB-6skb: Crystal Structure of Human Kallikrein 6 (N217D/I218Y/K224R) in co... -
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-Basic information
Entry | Database: PDB / ID: 6skb | ||||||
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Title | Crystal Structure of Human Kallikrein 6 (N217D/I218Y/K224R) in complex with GSK3496783A | ||||||
Components | Kallikrein-6KLK6 | ||||||
Keywords | HYDROLASE / Protease / Inhibitor / Complex | ||||||
Function / homology | Function and homology information tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å | ||||||
Authors | Thorpe, J.H. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Design and development of a series of borocycles as selective, covalent kallikrein 5 inhibitors. Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / ...Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / Polyakova, O. / Smith, K.J. / Thomas, P. / Thorpe, J.H. / Trottet, L. / Wang, Y. / Hovnanian, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6skb.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6skb.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 6skb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6skb ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skb | HTTPS FTP |
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-Related structure data
Related structure data | 6skcC 6skdC 1lo6S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 31407.521 Da / Num. of mol.: 3 / Mutation: N217D/I218Y/K224R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 27.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 100mM Tris-HCl pH 8.6, PEG 4000 18-28% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.975656 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975656 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→46.11 Å / Num. obs: 176516 / % possible obs: 98.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.055 / Rrim(I) all: 0.102 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 15911 / CC1/2: 0.599 / Rpim(I) all: 0.438 / Rrim(I) all: 0.804 / % possible all: 93.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LO6 Resolution: 1.84→36.51 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.135
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Displacement parameters | Biso max: 115.56 Å2 / Biso mean: 35.02 Å2 / Biso min: 11.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→36.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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