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Yorodumi- PDB-8i71: Hepatitis B virus core protein Y132A mutant in complex with Linve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i71 | ||||||
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Title | Hepatitis B virus core protein Y132A mutant in complex with Linvencorvir (RG7907), a Hepatitis B Virus (HBV) Core Protein Allosteric Modulator (CpAM) | ||||||
Components | Capsid proteinCapsid | ||||||
Keywords | VIRAL PROTEIN / capsid assembly inhibitor / ANTIVIRAL PROTEIN | ||||||
Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Hepatitis B virus subtype adyw | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Zhou, Z. / Xu, Z.H. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Discovery of Linvencorvir (RG7907), a Hepatitis B Virus Core Protein Allosteric Modulator, for the Treatment of Chronic HBV Infection. Authors: Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Shi, H. / Zhou, M. / Zhang, Z. / Kou, B. / Hu, T. / Zhou, Z. / Xu, Z. / Zhou, X. / Zhou, Y. / Tian, X. / Yang, G. / Young, J.A.T. / Qiu, H. / ...Authors: Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Shi, H. / Zhou, M. / Zhang, Z. / Kou, B. / Hu, T. / Zhou, Z. / Xu, Z. / Zhou, X. / Zhou, Y. / Tian, X. / Yang, G. / Young, J.A.T. / Qiu, H. / Ottaviani, G. / Xie, J. / Mayweg, A.V. / Shen, H.C. / Zhu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i71.cif.gz | 414 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i71.ent.gz | 346.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i71 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i71 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 17486.916 Da / Num. of mol.: 6 / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus subtype adyw / Production host: Escherichia coli (E. coli) / References: UniProt: P03147 |
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-Non-polymers , 6 types, 728 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-IPA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-OTI / #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM citrate, 21%(vol/vol) isopropanol, 1%(W/V) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 650539 / % possible obs: 95.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.811 / Num. unique obs: 160629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.513 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→33.513 Å
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Refine LS restraints |
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LS refinement shell |
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