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Yorodumi- PDB-1bgo: CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bgo | ||||||
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Title | CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR | ||||||
Components | CATHEPSIN K | ||||||
Keywords | HYDROLASE / SULFHYDRYL PROTEINASE / THIOL PROTEASE | ||||||
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: 2.3 Å | ||||||
Authors | Desjarlais, R.L. / Yamashita, D.S. / Oh, H.-J. / Bondinell, W.E. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B. / Smith, W.W. ...Desjarlais, R.L. / Yamashita, D.S. / Oh, H.-J. / Bondinell, W.E. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / D'Alessio, K. / Janson, C.A. / Mcqueney, M.S. / Tomaszek, T.A. / Levy, M.A. / Veber, D.F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1998 Title: Use of X-Ray Co-Crystal Structures and Molecular Modeling to Design Potent and Selective Non-Peptide Inhibitors of Cathepsin K Authors: Desjarlais, R.L. / Yamashita, D.S. / Oh, H.J. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B.G. / Smith, W.W. / Abdel-Meguid, S.S. / Dalessio, K. / Janson, C.A. ...Authors: Desjarlais, R.L. / Yamashita, D.S. / Oh, H.J. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B.G. / Smith, W.W. / Abdel-Meguid, S.S. / Dalessio, K. / Janson, C.A. / Mcqueney, M.S. / Tomaszek, T.A. / Levy, M.A. / Veber, D.F. #1: 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 | 1bgo.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bgo.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bgo_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 1bgo_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 1bgo_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1bgo_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bgo ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bgo | HTTPS FTP |
-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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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 COVALENTLY BOUND TO ACTIVE SITE CYS 25 / Source: (gene. exp.) Homo sapiens (human) / Cell: OSTEOCLAST / 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-I10 / |
#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: 2.95 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
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: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 11258 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.27 / % possible all: 54 |
Reflection shell | *PLUS % possible obs: 54 % |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 1ATK Resolution: 2.3→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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