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Yorodumi- PDB-1nl6: Crystal Structure Of The Cysteine Protease Human Cathepsin K In C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nl6 | ||||||
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Title | Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / SULFHYDRYL PROTEINASE | ||||||
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 / fibronectin binding / Collagen degradation / mitophagy / collagen catabolic process / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / apical plasma membrane / immune response / external side of plasma membrane / serine-type endopeptidase activity / cysteine-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: 2.8 Å | ||||||
Authors | Smith, W.W. / Janson, C.A. / Zhao, B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: Azepanone-based inhibitors of human and rat cathepsin K Authors: Marquis, R.W. / Ru, Y. / LoCastro, S.M. / Zeng, J. / Yamashita, D.S. / Oh, H.J. / Erhard, K.F. / Davis, L.D. / Tomaszek, T.A. / Tew, D. / Salyers, K. / Proksch, J. / Ward, K. / Smith, B. / ...Authors: Marquis, R.W. / Ru, Y. / LoCastro, S.M. / Zeng, J. / Yamashita, D.S. / Oh, H.J. / Erhard, K.F. / Davis, L.D. / Tomaszek, T.A. / Tew, D. / Salyers, K. / Proksch, J. / Ward, K. / Smith, B. / Levy, M. / Cummings, M.D. / Haltiwanger, R.C. / Trescher, G. / Wang, B. / Hemling, M.E. / Quinn, C.J. / Cheng, H.-Y. / Lin, F. / Smith, W.W. / Janson, C.A. / Zhao, B. / McQueney, M.S. / D'Alessio, K. / Lee, C.P. / Marzulli, A. / A Dodds, R. / Blake, S. / Hwang, S.M. / James, I.E. / Gress, C.J. / Bradley, B.R. / Lark, M.W. / Gowen, M. / Veber, D.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nl6.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nl6.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nl6 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nl6 | HTTPS FTP |
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-Related structure data
Related structure data | 1nljC 1atkS 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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Unit cell |
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-Components
#1: Protein | Mass: 23523.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K #2: Chemical | |
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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: 3.32 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 8000, 0.1 M imidazole, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→99 Å / Num. all: 19740 / Num. obs: 17372 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.58 / Rsym value: 0.58 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.55→2.59 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 9.9 / Num. unique all: 631 / Rsym value: 0.94 / % possible all: 65 |
Reflection | *PLUS Lowest resolution: 99 Å / % possible obs: 88 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATK Resolution: 2.8→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.83 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.01 |