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Yorodumi- PDB-3ao1: Fragment-based approach to the design of ligands targeting a nove... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ao1 | ||||||
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Title | Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase | ||||||
Components | POL polyprotein | ||||||
Keywords | VIRAL PROTEIN/TRANSFERASE INHIBITOR / DNA INTEGRATION / AIDS / INTEGRASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNaseH / Fragment binding / VIRAL PROTEIN-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wielens, J. / Parker, M.W. / Chalmers, D.K. / Scanlon, M.J. | ||||||
Citation | Journal: Chemmedchem / Year: 2011 Title: Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1 Authors: Wielens, J. / Headey, S.J. / Deadman, J.J. / Rhodes, D.I. / Parker, M.W. / Chalmers, D.K. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ao1.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ao1.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ao1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3ao1 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3ao1 | HTTPS FTP |
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-Related structure data
Related structure data | 3ao2C 3ao3C 3ao4C 3ao5C 3ovnC 3l3uS S: Starting model for refinement 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
#1: Protein | Mass: 17802.174 Da / Num. of mol.: 2 / Fragment: Integrase CATALYTIC CORE DOMAIN, 765-927 / Mutation: C56S, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: PeT23b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (de3) / References: UniProt: Q72498 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: 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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97937 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2007 Details: double crystal monochromator and K-B pair of biomorph mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62 Å / Num. all: 24972 / Num. obs: 24930 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.093 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.52 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L3U Resolution: 1.9→49.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.161 / 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: 38.818 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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