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Yorodumi- PDB-1atk: CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1atk | ||||||
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Title | CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhao, B. / Smith, W.W. / Janson, C.A. / Abdel-Meguid, S.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of human osteoclast cathepsin K complex with E-64. Authors: Zhao, B. / Janson, C.A. / Amegadzie, B.Y. / D'Alessio, K. / Griffin, C. / Hanning, C.R. / Jones, C. / Kurdyla, J. / McQueney, M. / Qiu, X. / Smith, W.W. / Abdel-Meguid, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1atk.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1atk.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 1atk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1atk_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 1atk_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 1atk_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1atk_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/1atk ftp://data.pdbj.org/pub/pdb/validation_reports/at/1atk | HTTPS FTP |
-Related structure data
Related structure data | 9papS S: Starting model for refinement |
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Similar structure data |
-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 Details: INHIBITOR E-64 COVALENT LINK BETWEEN INHIBITOR ATOM C2 AND THE SULFUR OF CYS 25 Source: (gene. exp.) Homo sapiens (human) / Cell: HUMAN OSTEOCLASTS / Cell line: SF21 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-E64 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.2 Details: PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion Temp details: room temp | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 25, 1995 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 10418 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.94 / Rsym value: 0.19 / % possible all: 80 |
Reflection | *PLUS Num. measured all: 33493 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 9PAP Resolution: 2.2→7 Å / Rfactor Rfree error: 0.095 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
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Refine analyze | Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8 / % reflection obs: 66.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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