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Yorodumi- PDB-3avf: Crystal structures of novel allosteric peptide inhibitors of HIV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3avf | ||||||
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Title | Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site | ||||||
Components |
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Keywords | RECOMBINATION/INHIBITOR / protein-protein interactions / HIV / RECOMBINATION-INHIBITOR 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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | Human immunodeficiency virus type 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Peat, T.S. / Deadman, J.J. / Newman, J. / Rhodes, D.I. | ||||||
Citation | Journal: Chembiochem / Year: 2011 Title: Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site. Authors: Rhodes, D.I. / Peat, T.S. / Vandegraaff, N. / Jeevarajah, D. / Newman, J. / Martyn, J. / Coates, J.A. / Ede, N.J. / Rea, P. / Deadman, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3avf.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3avf.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3avf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3avf_validation.pdf.gz | 483.5 KB | Display | wwPDB validaton report |
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Full document | 3avf_full_validation.pdf.gz | 494 KB | Display | |
Data in XML | 3avf_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3avf_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/3avf ftp://data.pdbj.org/pub/pdb/validation_reports/av/3avf | HTTPS FTP |
-Related structure data
Related structure data | 3av9C 3avaC 3avbC 3avcC 3avgC 3avhC 3aviC 3avjC 3avkC 3avlC 3avmC 3avnC C: citing same article (ref.) |
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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 ABDF
#1: Protein | Mass: 19685.273 Da / Num. of mol.: 2 / Fragment: CCD domain (UNP RESIDUES 1197-1359) / Mutation: C56S, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: NEW YORK-5 ISOLATE / Gene: gag-pol / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497 #2: Protein/peptide | Mass: 946.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthsis / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 182 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K PH range: 5.0-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→66.9 Å / Num. all: 41088 / Num. obs: 41088 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→61.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.579 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
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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 max: 75.91 Å2 / Biso mean: 21.9638 Å2 / Biso min: 6.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→61.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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