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Yorodumi- PDB-3zso: Small molecule inhibitors of the LEDGF site of HIV type 1 integra... -
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-Basic information
Entry | Database: PDB / ID: 3zso | ||||||
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Title | Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design | ||||||
Components | INTEGRASE | ||||||
Keywords | TRANSFERASE / AIDS | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Peat, T.S. / Newman, J. / Rhodes, D.I. / Deadman, J.J. / Vandergraaff, N. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A.V. / Thienthong, N. ...Peat, T.S. / Newman, J. / Rhodes, D.I. / Deadman, J.J. / Vandergraaff, N. / Le, G. / Jones, E.D. / Smith, J.A. / Coates, J.A.V. / Thienthong, N. / Dolezal, O. / Ryan, J.H. / Savage, G.P. / Francis, C.L. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design. Authors: Peat, T.S. / Rhodes, D.I. / Vandegraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / ...Authors: Peat, T.S. / Rhodes, D.I. / Vandegraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / Savage, G.P. / Francis, C.L. / 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 | 3zso.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zso.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zso ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zso | HTTPS FTP |
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-Related structure data
Related structure data | 3zcmC 3zsqC 3zsrC 3zsvC 3zswC 3zsxC 3zsyC 3zszC 3zt0C 3zt1C 3zt2C 3zt3C 3zt4C 3nf7S 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 18395.842 Da / Num. of mol.: 2 / Fragment: CORE CATALYTIC DOMAIN, RESIDUES 56-212 / Mutation: YES Source method: isolated from a genetically manipulated source Details: INHIBITOR BOUND TO THE LEDGF SITE / Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS / Strain: TYPE 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q76353, UniProt: P12497*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 182 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACY / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 56 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 139 TO ASP ...ENGINEERED |
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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: 2.45 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.7 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→61.5 Å / Num. obs: 38159 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NF7 Resolution: 1.75→61.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.984 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 189-192 ARE DISORDERED. SULFATE IONS AND OTHER HET ATOMS BESIDES THE KNOWN LIGAND ARE BEST GUESSES BASED ON THE CRYSTALLIZATION AND CRYO CONDITIONS.
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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: 25.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→61.54 Å
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Refine LS restraints |
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