[English] 日本語
Yorodumi- PDB-6pix: Crystal structure of HCV NS3/4A D168A protease in complex with P4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pix | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of HCV NS3/4A D168A protease in complex with P4-P5-5 (WK-25) | ||||||||||||
Components | NS3/4A protease | ||||||||||||
Keywords | hydrolase/hydrolase inhibitor / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex / HYDROLASE | ||||||||||||
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: 1.87 Å | ||||||||||||
Authors | Zephyr, J. / Schiffer, C.A. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Mbio / Year: 2020 Title: Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. Authors: Matthew, A.N. / Zephyr, J. / Nageswara Rao, D. / Henes, M. / Kamran, W. / Kosovrasti, K. / Hedger, A.K. / Lockbaum, G.J. / Timm, J. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pix.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pix.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pix_validation.pdf.gz | 818.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pix_full_validation.pdf.gz | 823.1 KB | Display | |
Data in XML | 6pix_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6pix_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/6pix ftp://data.pdbj.org/pub/pdb/validation_reports/pi/6pix | HTTPS FTP |
-Related structure data
Related structure data | 6piuC 6pivC 6piwC 6piyC 6pizC 6pj0C 6pj1C 6pj2C 6ue3C 5vojS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23348.418 Da / Num. of mol.: 1 / Mutation: D168A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4WYC6 |
---|
-Non-polymers , 5 types, 184 molecules
#2: Chemical | ChemComp-ZN / |
---|---|
#3: Chemical | ChemComp-OLY / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 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: 1.87→50 Å / Num. obs: 15984 / % possible obs: 98.1 % / Redundancy: 6.9 % / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.87→1.9 Å / Num. unique obs: 700 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VOJ Resolution: 1.87→23.88 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.45
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→23.88 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|