[English] 日本語
![](img/lk-miru.gif)
- PDB-2o8m: Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2o8m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease | ||||||
![]() | (Protease) x 2 | ||||||
![]() | VIRAL PROTEIN / SERINE PROTEASE / NS3 / NS4A / HEPATITIS C VIRUS | ||||||
Function / homology | ![]() positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / ribonucleoside triphosphate phosphatase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / lipid droplet / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to 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 / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fischmann, T.O. / Prongay, A.J. / Madison, V.M. / Yao, N. | ||||||
![]() | ![]() Title: Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6- ...Title: Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization Authors: Prongay, A.J. / Guo, Z. / Yao, N. / Pichardo, J. / Fischmann, T. / Strickland, C. / Myers, J. / Weber, P.C. / Beyer, B.M. / Ingram, R. / Hong, Z. / Prosise, W.W. / Ramanathan, L. / Taremi, S. ...Authors: Prongay, A.J. / Guo, Z. / Yao, N. / Pichardo, J. / Fischmann, T. / Strickland, C. / Myers, J. / Weber, P.C. / Beyer, B.M. / Ingram, R. / Hong, Z. / Prosise, W.W. / Ramanathan, L. / Taremi, S.S. / Yarosh-Tomaine, T. / Zhang, R. / Senior, M. / Yang, R.S. / Malcolm, B. / Arasappan, A. / Bennett, F. / Bogen, S.L. / Chen, K. / Jao, E. / Liu, Y.T. / Lovey, R.G. / Saksena, A.K. / Venkatraman, S. / Girijavallabhan, V. / Njoroge, F.G. / Madison, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.5 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oboC ![]() 2obqC ![]() 2oc0C ![]() 2oc1C ![]() 2oc7C ![]() 2oc8C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21217.225 Da / Num. of mol.: 2 / Mutation: S149A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9ELS8, UniProt: P27958*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein/peptide | Mass: 2410.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P27958 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.21 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.25 to 1.5M NaCl, 0.1 M MES, .1M Na/K PO4, 5mM beta-mercaptoethanol, pH 5.6-6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 46014 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -1 / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Rsym value: 0.0489 / Χ2: 0.887 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1429 / Χ2: 1.015 / % possible all: 58.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.674 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2 Å / Rfactor Rfree: 0.2688 / Rfactor Rwork: 0.2356 |