[English] 日本語
Yorodumi- PDB-5etx: Crystal structure of HCV NS3/4A protease A156T variant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5etx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-Linear (MK-5172 linear analogue) | |||||||||
Components | NS3 protease | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / macrocyclization / MK-5172 analogue / grazoprevir / HCV protease inhibitor resistance / 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 | Hepatitis C virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | |||||||||
Authors | Soumana, D. / Yilmaz, N.K. / Ali, A. / Prachanronarong, K.L. / Aydin, C. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
| |||||||||
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. #2: Journal: PLoS Pathog. / Year: 2012 Title: The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5etx.cif.gz | 275.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5etx.ent.gz | 221.5 KB | Display | PDB format |
PDBx/mmJSON format | 5etx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/5etx ftp://data.pdbj.org/pub/pdb/validation_reports/et/5etx | HTTPS FTP |
---|
-Related structure data
Related structure data | 5epnC 5epyC 5eqqC 3m5mS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||
4 |
| |||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 20646.334 Da / Num. of mol.: 4 / Mutation: A156T, S139C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Plasmid: pET28a / Cell line (production host): BL21-DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: C1KIK8 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-5RS / ~{ #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -k,-h,-l / Fraction: 0.08 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→30 Å / Num. obs: 31801 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Χ2: 1.389 / Net I/av σ(I): 17.763 / Net I/σ(I): 18.4 / Num. measured all: 129154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M5M Resolution: 2.35→27.528 Å / FOM work R set: 0.8071 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.28 Å2 / Biso mean: 24.78 Å2 / Biso min: 3.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→27.528 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|