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- PDB-1n1l: CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n1l | ||||||
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Title | CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X) | ||||||
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![]() | VIRAL PROTEIN / SERINE PROTEASE / NONSTRUCTURAL PROTEINS / COFACTOR PEPTIDE / HELICASE / INHIBITOR | ||||||
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 / viral process / endoplasmic reticulum-Golgi intermediate compartment membrane / virion component / 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 / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Andrews, D.M. / Chaignot, H. / Coomber, B.A. / Good, A.C. / Hind, S.L. / Jones, P.S. / Mill, G. / Robinson, J.E. / Skarzynski, T. / Slater, M.J. / Somers, D.O.N. | ||||||
![]() | ![]() Title: Pyrrolidine-5,5-trans-lactams. 2. The use of X-ray Crystal Structure Data in the Optimisation of P3 and P4 Substituents Authors: Andrews, D.M. / Chaignot, H. / Coomber, B.A. / Good, A.C. / Hind, S.L. / Johnson, M.R. / Jones, P.S. / Mill, G. / Robinson, J.E. / Skarzynski, T. / Slater, M.J. / Somers, D.O.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488 KB | Display | ![]() |
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Full document | ![]() | 494.1 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 21044.975 Da / Num. of mol.: 2 / Fragment: Protease domain / Mutation: A164T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2394.039 Da / Num. of mol.: 2 / Fragment: Residues 21-39 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the protein is naturally found in HEPATITIS C VIRUS type 1B. References: GenBank: 5748511, UniProt: O39914*PLUS #3: Chemical | #4: Chemical | ChemComp-TRL / { | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Inhibitor soaked into crystal generated according to Kim et al. (1996) Cell, 87, 343-355, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
Crystal grow | *PLUS Details: Kim, J.L., (1996) 8, 344. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 22723 / Num. obs: 21878 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2074 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 40 Å |
Reflection shell | *PLUS % possible obs: 92 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.569 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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