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Yorodumi- PDB-3h7d: The crystal structure of the cathepsin K Variant M5 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h7d | |||||||||
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Title | The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate | |||||||||
Components | Cathepsin K | |||||||||
Keywords | HYDROLASE / glycosaminoglycan / sulfhydryl peptidase / cathepsin K mutant / ternary complex / Disease mutation / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen | |||||||||
Function / homology | Function and homology information cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / autophagy of mitochondrion / Activation of Matrix Metalloproteinases / Collagen degradation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / cysteine-type endopeptidase activator activity involved in apoptotic process / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / bone resorption / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / extracellular region / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.242 Å | |||||||||
Authors | Cherney, M.M. / Kienetz, M. / Bromme, D. / James, M.N.G. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure-activity analysis of cathepsin K/chondroitin 4-sulfate interactions. Authors: Cherney, M.M. / Lecaille, F. / Kienitz, M. / Nallaseth, F.S. / Li, Z. / James, M.N. / Bromme, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h7d.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7d.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7d ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7d | HTTPS FTP |
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-Related structure data
Related structure data | 1atkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Details | monomer |
-Components
#1: Protein | Mass: 23459.307 Da / Num. of mol.: 2 / Fragment: UNP residues 115-329 / Mutation: K9E, I171E, Q172S, N190M, K191G, L195K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K #2: Polysaccharide | 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2- ...2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE OLIGOSACCHARIDE CHAIN (BDP-ASG)N IS CONTINUOUS. IT IS RUNNING THROUGH THE SEVERAL UNIT CELLS. ...THE OLIGOSACCH | |
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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: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 24791 / Num. obs: 24692 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ATK Resolution: 2.242→40.245 Å / SU ML: 0.9 / σ(F): 1.34 / Phase error: 23.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.713 Å2 / ksol: 0.411 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.242→40.245 Å
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Refine LS restraints |
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LS refinement shell |
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