+Open data
-Basic information
Entry | Database: PDB / ID: 7y0e | ||||||
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Title | Crystal structure of TMPRSS2 in complex with Camostat | ||||||
Components | (Transmembrane protease serine 2 catalytic ...) x 2 | ||||||
Keywords | HYDROLASE / Inhibitor / Complex / Host / Antiviral / ANTIVIRAL PROTEIN | ||||||
Function / homology | Function and homology information transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Wang, H. / Duan, Y. / Liu, X. / 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 | 7y0e.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y0e.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y0e_validation.pdf.gz | 944.4 KB | Display | wwPDB validaton report |
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Full document | 7y0e_full_validation.pdf.gz | 952.9 KB | Display | |
Data in XML | 7y0e_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 7y0e_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/7y0e ftp://data.pdbj.org/pub/pdb/validation_reports/y0/7y0e | HTTPS FTP |
-Related structure data
Related structure data | 7xydC 7y0fC 8hd8C 8he9C 8heiC 8henC 8hetC 8hfvC 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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2 |
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Unit cell |
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-Components
-Transmembrane protease serine 2 catalytic ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 16054.661 Da / Num. of mol.: 2 / Mutation: Residues 250-255 SSRQSR were replaced with DDDDK. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393 #2: Protein | Mass: 27856.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393 |
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-Sugars , 1 types, 2 molecules
#3: Sugar |
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-Non-polymers , 4 types, 159 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | Chains A and C, as well as B and D, were manipulated as one single peptide, but auto-cleaved at ...Chains A and C, as well as B and D, were manipulated as one single peptide, but auto-cleaved at residue 256 during zymogen activation. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % / Description: Plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M acetic acid/sodium acetate, pH 5.0, 16% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 10, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→45.46 Å / Num. obs: 32630 / % possible obs: 99.5 % / Redundancy: 4.02 % / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.119 / Net I/σ(I): 10.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model predicted by Alphafold Resolution: 2.39→45.46 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.72 / 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: 2.39→45.46 Å
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Refine LS restraints |
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LS refinement shell |
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