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Yorodumi- PDB-1mem: Crystal structure of Cathepsin K complexed with a potent vinyl su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mem | ||||||
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Title | Crystal structure of Cathepsin K complexed with a potent vinyl sulfone inhibitor | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / OSTEOPOROSIS / PROTEASE / DRUG DESIGN / CYSTEINE / OSTEOCLAST / Disease mutation / Disulfide bond / Glycoprotein / Lysosome / Thiol protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / mitophagy / fibronectin binding / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cysteine-type peptidase activity / 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 / positive regulation of apoptotic signaling pathway / 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 / intracellular membrane-bounded organelle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mcgrath, M.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of human cathepsin K complexed with a potent inhibitor. Authors: McGrath, M.E. / Klaus, J.L. / Barnes, M.G. / Bromme, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mem.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mem.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mem_validation.pdf.gz | 814.7 KB | Display | wwPDB validaton report |
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Full document | 1mem_full_validation.pdf.gz | 816.9 KB | Display | |
Data in XML | 1mem_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1mem_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1mem ftp://data.pdbj.org/pub/pdb/validation_reports/me/1mem | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23523.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-0D6 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | INHIBITOR 4-METHYLPIPERAZINE-1-CARBOXYLIC ACID [1-[(3-BENZENESULFONYL-1-PHENETHYLALLYL)CARBAMOYL]-2- ...INHIBITOR 4-METHYLPIPE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 6 / Details: MG FORMATE, UNBUFFERED, pH 6.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 20293 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.073 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.17 / % possible all: 68 |
Reflection | *PLUS Num. measured all: 75667 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 68 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODEL FOR CATHEPSIN K (MEM, UNPUBLISHED RESULTS) Resolution: 1.8→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2 /
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.183 |