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Open data
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Basic information
Entry | Database: PDB / ID: 3wne | ||||||
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Title | Cyclic hexapeptide PKIDNG in complex with HIV-1 integrase | ||||||
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![]() | Viral Protein/Peptide / DNA INTEGRATION / AIDS / INTEGRASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNASEH / LEDGF / LENS EPITHELIUM DERIVED GROWTH FACTOR / Viral Protein-Peptide 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 | ![]() ![]() ![]() | ||||||
![]() | Wielens, J. / Chalmers, D.K. / Parker, M.W. | ||||||
![]() | ![]() Title: Hexapeptide mimetics of LEDGF in complex with HIV-1 integrase Authors: Northfield, S.E. / Wielens, J. / Headey, S.J. / Mulcair, M. / Scanlon, M.J. / Parker, M.W. / Thompson, P.E. / Chalmers, D.K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.4 KB | Display | ![]() |
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Full document | ![]() | 466.7 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wnfC ![]() 3wngC ![]() 3wnhC ![]() 3l3uS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 17101.393 Da / Num. of mol.: 2 / Fragment: Catalytic core domain, UNP residue 1203-1359 / Mutation: C56S, S123G, T124A, K127R, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | |
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-Non-polymers , 4 types, 129 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5mM CADMIUM CHLORIDE , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2009 / Details: Mirrors |
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.7 Å / Num. all: 29655 / Num. obs: 29394 / % possible obs: 99.1 % / Observed criterion σ(I): 166415 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4235 / Rsym value: 0.459 / % possible all: 86.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3L3U Resolution: 1.7→39.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.598 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.7 Å
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