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Yorodumi- PDB-3ao5: Fragment-based approach to the design of ligands targeting a nove... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ao5 | |||||||||
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Title | Fragment-based approach to the design of ligands targeting a novel site on 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 stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / aspartic-type endopeptidase activity / DNA recombination / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / aspartic-type endopeptidase activity / DNA recombination / 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: 1.8 Å | |||||||||
Authors | Wielens, J. / Headey, S.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 | 3ao5.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ao5.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ao5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ao5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3ao5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3ao5_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3ao5_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3ao5 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3ao5 | HTTPS FTP |
-Related structure data
Related structure data | 3ao1C 3ao2C 3ao3C 3ao4C 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
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 17770.137 Da / Num. of mol.: 2 Fragment: Integrase CATALYTIC CORE DOMAIN, UNP residues 765-927 Mutation: C56S, S123G, T124A, K127R, 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 / References: UniProt: Q72498 #2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | |
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-Non-polymers , 5 types, 74 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CD / #7: 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: 2.03 Å3/Da / Density % sol: 39.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8M AmSO4, 0.15M Na Citrate pH 4.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.957 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2008 / Details: Mirrors |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.957 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.8 Å / Num. all: 25903 / Num. obs: 25633 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Rsym value: 0.06 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.294 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L3U Resolution: 1.8→34.57 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.162 / 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: 24.804 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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