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Yorodumi- PDB-5epy: Crystal structure of HCV NS3/4A protease A156T variant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5epy | |||||||||
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Title | Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-mcP1P3 (MK-5172 P1-P3 macrocyclic analogue) | |||||||||
Components | NS3 protease | |||||||||
Keywords | HYDROLASE / grazoprevir analogue / macrocycle / drug resistance / HCV protease inhibitor / MK-5172 | |||||||||
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 | Hepatitis C virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Soumana, D.I. / Yilmaz, N.K. / Ali, A. / Prachanronarong, K.L. / Aydin, C. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172. Authors: Soumana, D.I. / Kurt Yilmaz, N. / Prachanronarong, K.L. / Aydin, C. / Ali, A. / Schiffer, C.A. #1: Journal: ACS Chem. Biol. / Year: 2013 Title: Evaluating the role of macrocycles in the susceptibility of hepatitis C virus NS3/4A protease inhibitors to drug resistance. Authors: Ali, A. / Aydin, C. / Gildemeister, R. / Romano, K.P. / Cao, H. / Ozen, A. / Soumana, D. / Newton, A. / Petropoulos, C.J. / Huang, W. / 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 | 5epy.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5epy.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 5epy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5epy ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5epy | HTTPS FTP |
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-Related structure data
Related structure data | 5epnC 5eqqC 5etxC 3m5mS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 21031.838 Da / Num. of mol.: 1 / Mutation: A156T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: C1KIK8 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-5R2 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES buffer pH 6.5, 4% (w/v) ammonium sulfate, 20-26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→35 Å / Num. obs: 9070 / % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.075 / Net I/av σ(I): 22.401 / Net I/σ(I): 9.1 / Num. measured all: 39511 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3m5m Resolution: 2.3→35 Å / Cross valid method: FREE R-VALUE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso max: 71.59 Å2 / Biso mean: 20.3824 Å2 / Biso min: 7.63 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35 Å
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