+Open data
-Basic information
Entry | Database: PDB / ID: 8he9 | ||||||
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Title | Crystal structure of CTSB in complex with K777 | ||||||
Components | Cathepsin B | ||||||
Keywords | ANTIVIRAL PROTEIN/INHIBITOR / inhibitor / antiviral / protease / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Wang, H. / Li, D. / Sun, L. / Yang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry. Authors: Wang, H. / Yang, Q. / Liu, X. / Xu, Z. / Shao, M. / Li, D. / Duan, Y. / Tang, J. / Yu, X. / Zhang, Y. / Hao, A. / Wang, Y. / Chen, J. / Zhu, C. / Guddat, L. / Chen, H. / Zhang, L. / Chen, X. ...Authors: Wang, H. / Yang, Q. / Liu, X. / Xu, Z. / Shao, M. / Li, D. / Duan, Y. / Tang, J. / Yu, X. / Zhang, Y. / Hao, A. / Wang, Y. / Chen, J. / Zhu, C. / Guddat, L. / Chen, H. / Zhang, L. / Chen, X. / Jiang, B. / Sun, L. / Rao, Z. / Yang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8he9.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8he9.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 8he9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8he9_validation.pdf.gz | 854.7 KB | Display | wwPDB validaton report |
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Full document | 8he9_full_validation.pdf.gz | 855.6 KB | Display | |
Data in XML | 8he9_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 8he9_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8he9 ftp://data.pdbj.org/pub/pdb/validation_reports/he/8he9 | HTTPS FTP |
-Related structure data
Related structure data | 7xydC 7y0eC 7y0fC 8hd8C 8heiC 8henC 8hetC 8hfvC 6ay2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27972.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Production host: Escherichia coli (E. coli) / References: UniProt: P07858, cathepsin B | ||||||
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#2: Chemical | ChemComp-0IW / | ||||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 17.1 % v/v Polyethylene glycol 600, 50 mM MES pH 5.6, 8.6 % w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 10, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→39.03 Å / Num. obs: 31146 / % possible obs: 99.9 % / Redundancy: 13.26 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Net I/σ(I): 23.75 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AY2 Resolution: 1.55→39.03 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→39.03 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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