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- PDB-4a1x: Co-Complex structure of NS3-4A protease with the inhibitory pepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a1x | ||||||
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Title | Co-Complex structure of NS3-4A protease with the inhibitory peptide CP5-46-A (Synchrotron data) | ||||||
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![]() | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / UNMODIFIED INHIBITORY PEPTIDES | ||||||
Function / homology | ![]() RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / RNA strand annealing activity / 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 ...RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / RNA strand annealing activity / 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 / protein-DNA complex / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmelz, S. / Kuegler, J. / Collins, J. / Heinz, D. | ||||||
![]() | ![]() Title: High Affinity Peptide Inhibitors of the Hepatitis C Virus Ns3-4A Protease Refractory to Common Resistant Mutants. Authors: Kugler, J. / Schmelz, S. / Gentzsch, J. / Haid, S. / Pollmann, E. / Van Den Heuvel, J. / Franke, R. / Pietschmann, T. / Heinz, D.W. / Collins, J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 462.5 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a1tC ![]() 4a1vC ![]() 1dxpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21385.422 Da / Num. of mol.: 2 / Fragment: RESIDUES 1678-1690,1028-1206 Source method: isolated from a genetically manipulated source Details: FUSION PROTEIN OF 4A (1678-1690) WITH NS3 (1028-1206) Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P26662, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase #2: Protein/peptide | Mass: 2304.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DERIVED FROM PEPTIDE LIBRARY / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE DISCREPANCIES HAVE BEEN INDICATED BY AUTHOR AS NATURAL VARIANTS, AS THE REPLICON WAS ...SEQUENCE DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % / Description: NONE |
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Crystal grow | Details: 0.1 M MES PH 6.0 OR 0.1 M NA CITRATE PH 5.1 AND 2.2M KCL, 5% ISOPROPANOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80.8 Å / Num. obs: 32044 / % possible obs: 99.6 % / Observed criterion σ(I): 2.7 / Redundancy: 3.7 % / Biso Wilson estimate: 30.17 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DXP Resolution: 1.9→80.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.319 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.089 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→80.82 Å
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