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Yorodumi- PDB-3ovn: Fragment-based approach to the design of ligands targeting a nove... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ovn | |||||||||
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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 / DNA recombination / aspartic-type endopeptidase activity / 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 / 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: 1.95 Å | |||||||||
Authors | Wielens, J. / Chalmers, D.K. / Headey, S.J. / Deadman, J.J. / Rhodes, D.K. / Parker, M.W. / 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 | 3ovn.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ovn.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ovn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ovn_validation.pdf.gz | 839.5 KB | Display | wwPDB validaton report |
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Full document | 3ovn_full_validation.pdf.gz | 844.4 KB | Display | |
Data in XML | 3ovn_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3ovn_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/3ovn ftp://data.pdbj.org/pub/pdb/validation_reports/ov/3ovn | HTTPS FTP |
-Related structure data
Related structure data | 3ao1C 3ao2C 3ao3C 3ao4C 3ao5C 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: 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: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | |
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-Non-polymers , 4 types, 65 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CD / #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: 2.05 Å3/Da / Density % sol: 39.98 % |
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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: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2007 / Details: K-B pair of biomorph mirrors |
Radiation | Monochromator: double crystal monochromator and K-B pair of biomorph mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.25 Å / Num. all: 23203 / Num. obs: 21811 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.38 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.112 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3184 / Rsym value: 0.479 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L3U Resolution: 1.95→40.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.656 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / 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: 25.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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