[English] 日本語
Yorodumi- PDB-6vdm: HCV NS3/4A protease A156T, D168E double mutant in complex with gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vdm | ||||||
---|---|---|---|---|---|---|---|
Title | HCV NS3/4A protease A156T, D168E double mutant in complex with glecaprevir | ||||||
Components | Non-structural protein 4A, Serine protease NS3 | ||||||
Keywords | VIRAL PROTEIN / Hydrolase / HCV protease / NS34A protease / glecaprevir | ||||||
Function / homology | Function and homology information hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus genotype 1a | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Timm, J. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: RAS at position 156 of HCV NS3/4A protease abolish inhibition by current HCV drugs Authors: Timm, J. / Zephyr, J. / Hou, S. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vdm.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vdm.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vdm_validation.pdf.gz | 382 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vdm_full_validation.pdf.gz | 385 KB | Display | |
Data in XML | 6vdm_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6vdm_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/6vdm ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vdm | HTTPS FTP |
-Related structure data
Related structure data | 6vdlC 6p6mS 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: 21563.445 Da / Num. of mol.: 1 Mutation: C1679S, V1686I, V1687N, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, Q1106K, P1112Q, A1182T, N1200S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus genotype 1a (isolate 1) Strain: isolate 1 / Production host: Escherichia coli (E. coli) References: UniProt: P26664, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase |
---|
-Non-polymers , 5 types, 196 molecules
#2: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#3: Chemical | ChemComp-O31 / ( | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.56 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.5 2% Ammonium sulfate 20-25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→23.71 Å / Num. obs: 15654 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.962 / Net I/σ(I): 42.23 |
Reflection shell | Resolution: 1.898→1.966 Å / Num. unique obs: 1499 / CC1/2: 0.998 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6p6m Resolution: 1.9→23.71 Å / SU ML: 0.1495 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3038
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→23.71 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -4.11637586013 Å / Origin y: -21.8964048061 Å / Origin z: 9.04448898556 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |