+Open data
-Basic information
Entry | Database: PDB / ID: 3wnf | ||||||
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Title | Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase | ||||||
Components |
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Keywords | 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 | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Wielens, J. / Chalmers, D.K. / Parker, M.W. | ||||||
Citation | Journal: to be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wnf.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wnf.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wnf_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 3wnf_full_validation.pdf.gz | 474.1 KB | Display | |
Data in XML | 3wnf_validation.xml.gz | 15 KB | Display | |
Data in CIF | 3wnf_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wnf ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wnf | HTTPS FTP |
-Related structure data
Related structure data | 3wneC 3wngC 3wnhC 3l3uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Human immunodeficiency virus type 1 / Strain: NL43 / Gene: HIV-1 POL / Plasmid: PET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12497 #2: Protein/peptide | |
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-Non-polymers , 4 types, 160 molecules
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 51039 / Num. obs: 48158 / % possible obs: 94.4 % / Observed criterion σ(I): 263341 / Redundancy: 5.5 % / Rmerge(I) obs: 0.038 / Rsym value: 0.043 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.7 / Num. unique all: 23206 / Rsym value: 0.471 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L3U Resolution: 1.45→43.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.343 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / 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: 17.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→43.36 Å
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