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Yorodumi- PDB-7l7n: Crystal structure of HCV NS3/4A D168A protease in complex with NR02-59 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l7n | |||||||||
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Title | Crystal structure of HCV NS3/4A D168A protease in complex with NR02-59 | |||||||||
Components | NS3 protease | |||||||||
Keywords | HYDROLASE/INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex / HYDROLASE / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Hepacivirus C | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | |||||||||
Authors | Zephyr, J. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. Authors: Nageswara Rao, D. / Zephyr, J. / Henes, M. / Chan, E.T. / Matthew, A.N. / Hedger, A.K. / Conway, H.L. / Saeed, M. / Newton, A. / Petropoulos, C.J. / Huang, W. / Kurt Yilmaz, N. / Schiffer, C.A. / Ali, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l7n.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l7n.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 7l7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/7l7n ftp://data.pdbj.org/pub/pdb/validation_reports/l7/7l7n | HTTPS FTP |
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-Related structure data
Related structure data | 7l7lC 7l7oC 7l7pC 5vojS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23486.564 Da / Num. of mol.: 1 / Mutation: D168A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4WYC6 |
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-Non-polymers , 5 types, 201 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-XSV / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 2.06 Å3/Da / Density % sol: 40.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350 The crystals were then soaked overnight in cryogenic conditions containing inhibitor (100 mM MES Buffer pH 6.5, 4% (W/V) ...Details: 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350 The crystals were then soaked overnight in cryogenic conditions containing inhibitor (100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350, 15% Ethylene glycol, and 10-20 mM of inhibitor in DMF) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→24.0555 Å / Num. obs: 26388 / % possible obs: 98.55 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.22 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 1.59→1.647 Å / Num. unique obs: 2355 / CC1/2: 0.838 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VOJ Resolution: 1.59→24.05 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3013 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→24.05 Å
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Refine LS restraints |
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LS refinement shell |
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