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- PDB-1ayu: CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ayu | ||||||
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Title | CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC BISCARBOHYDRAZIDE INHIBITOR | ||||||
![]() | CATHEPSIN K | ||||||
![]() | HYDROLASE / SULFHYDRYL PROTEINASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhao, B. / Smith, W.W. / Janson, C.A. / Abdel-Meguid, S.S. | ||||||
![]() | ![]() Title: Design of potent and selective human cathepsin K inhibitors that span the active site. Authors: Thompson, S.K. / Halbert, S.M. / Bossard, M.J. / Tomaszek, T.A. / Levy, M.A. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Amegadzie, B.Y. ...Authors: Thompson, S.K. / Halbert, S.M. / Bossard, M.J. / Tomaszek, T.A. / Levy, M.A. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Amegadzie, B.Y. / Hanning, C.R. / DesJarlais, R.L. / Briand, J. / Sarkar, S.K. / Huddleston, M.J. / Ijames, C.F. / Carr, S.A. / Garnes, K.T. / Shu, A. / Heys, J.R. / Bradbeer, J. / Zembryki, D. / Lee-Rykaczewski, L. / James, I.E. / Lark, M.W. / Drake, F.H. / Gowen, M. / Gleason, J.G. / Veber, D.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.2 KB | Display | ![]() |
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PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ayvC ![]() 1aywC ![]() 1atkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-INA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.5 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 30% MPD, 0.1M MES, 0.1M TRIS-HCL, PH7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1996 / Details: COLLIMATOR |
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: 9452 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.22→2.44 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4 / Rsym value: 0.24 / % possible all: 93 |
Reflection shell | *PLUS % possible obs: 93 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ATK Resolution: 2.2→6 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / 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: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.29 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.254 |