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Yorodumi- PDB-6dis: Crystal structure of HCV NS3/4A protease in complex with P4-1 (AJ-71) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dis | |||||||||
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Title | Crystal structure of HCV NS3/4A protease in complex with P4-1 (AJ-71) | |||||||||
Components | NS3 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: 1.921 Å | |||||||||
Authors | Matthew, A.N. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Design of Hepatitis C NS3/4A Protease Inhibitors Leveraging Untapped Regions of the Substrate Envelope Authors: Matthew, A.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 | 6dis.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dis.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dis_validation.pdf.gz | 840.8 KB | Display | wwPDB validaton report |
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Full document | 6dis_full_validation.pdf.gz | 845.6 KB | Display | |
Data in XML | 6dis_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6dis_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/6dis ftp://data.pdbj.org/pub/pdb/validation_reports/di/6dis | HTTPS FTP |
-Related structure data
Related structure data | 6diqC 6dirC 6ditC 6diuC 6divC 6diwC 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: 21175.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4WYC6 |
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-Non-polymers , 5 types, 225 molecules
#2: Chemical | ChemComp-GKG / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.31 Å3/Da / Density % sol: 46.71 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Dec 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.921→23.171 Å / Num. obs: 14999 / % possible obs: 96.7 % / Redundancy: 7.1 % / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.9214→2.0696 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VOJ Resolution: 1.921→23.171 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.921→23.171 Å
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Refine LS restraints |
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LS refinement shell |
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