+Open data
-Basic information
Entry | Database: PDB / ID: 7mm8 | |||||||||
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Title | Crystal structure of HCV NS3/4A protease in complex with NR02-08 | |||||||||
Components | NS3/4a protease | |||||||||
Keywords | HYDROLASE/INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / 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: 1.43 Å | |||||||||
Authors | Zephyr, J. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. Authors: Zephyr, J. / Nageswara Rao, D. / Vo, S.V. / Henes, M. / Kosovrasti, K. / Matthew, A.N. / Hedger, A.K. / Timm, J. / Chan, E.T. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mm8.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mm8.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/7mm8 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/7mm8 | HTTPS FTP |
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-Related structure data
Related structure data | 7mm2C 7mm3C 7mm4C 7mm5C 7mm6C 7mm7C 7mm9C 7mmaC 7mmbC 7mmcC 7mmdC 7mmfC 7mmgC 7mmhC 7mmiC 7mmjC 7mmkC 7mmlC 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: 21349.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4WYC6, hepacivirin |
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-Non-polymers , 5 types, 235 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-ZJM / ( | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / | #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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, pH 6.5, 4% w/v ammonium sulfate, 20-26% PEG3350, cryoprotectant = same + 15% ethylene glycol |
-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: Jun 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→26.28 Å / Num. obs: 47936 / % possible obs: 97.74 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.973 / Net I/σ(I): 16.57 |
Reflection shell | Resolution: 1.43→1.481 Å / Num. unique obs: 4388 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5VOJ Resolution: 1.43→26.28 Å / SU ML: 0.1171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7368 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: 21.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→26.28 Å
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Refine LS restraints |
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LS refinement shell |
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