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- PDB-4y1c: Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y1c | ||||||
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Title | Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain | ||||||
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![]() | TRANSFERASE/TRANSFERASE BINDING PROTEIN / DNA INTEGRATION / AIDS / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNASEH / LEDGF / LENS EPITHELIUM DERIVED GROWTH FACTOR / VIRAL PROTEIN-PEPTIDE COMPLEX / TRANSFERASE-TRANSFERASE BINDING PROTEIN 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 / endonuclease activity / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wielens, J. / Chalmers, D.K. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.9 KB | Display | ![]() |
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PDB format | ![]() | 52.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y1dC ![]() 3wneS 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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Unit cell |
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Components
#1: Protein | Mass: 18215.648 Da / Num. of mol.: 2 / Fragment: residues 50-212 / Mutation: C56S, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 737.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CD / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.83 % |
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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 REMARK 280 CITRATE, 5MM CADMIUM CHLORIDE, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 13118 / % possible obs: 93.5 % / Redundancy: 6.93 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 7.23 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 8.32 / % possible all: 81.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WNE Resolution: 2.3→28.35 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.835 / SU B: 7.836 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.35 Å
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Refine LS restraints |
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