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- PDB-4qnb: Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qnb | ||||||
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Title | Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PHENYLALANINAMIDE inhibitor | ||||||
![]() | CAPSID PROTEIN P24 | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / capsid protein / disulfide crosslink / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pornillos, O. | ||||||
![]() | ![]() Title: Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Authors: Bhattacharya, A. / Alam, S.L. / Fricke, T. / Zadrozny, K. / Sedzicki, J. / Taylor, A.B. / Demeler, B. / Pornillos, O. / Ganser-Pornillos, B.K. / Diaz-Griffero, F. / Ivanov, D.N. / Yeager, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.4 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.6 KB | Display | ![]() |
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Full document | ![]() | 789.2 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wymC ![]() 3h47S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: A14C,E45C,W184A,M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Plasmid: pET11a / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-1B0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 8,000, 2% Tacsimate, 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→50 Å / Num. obs: 18424 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.087 / Net I/σ(I): 43.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3h47 Resolution: 1.996→26.642 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.996→26.642 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 24.8716 Å / Origin y: 10.3507 Å / Origin z: -0.7647 Å
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Refinement TLS group | Selection details: all |