+Open data
-Basic information
Entry | Database: PDB / ID: 8zh4 | ||||||
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Title | HIV-1 integrase core domain in complex with compound 5 | ||||||
Components | Integrase | ||||||
Keywords | VIRAL PROTEIN / HIV / integrase / inhibitor | ||||||
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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Furuzono, T. / Orita, T. / Nomura, A. / Adachi, T. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2024 Title: Design and synthesis of novel and potent allosteric HIV-1 integrase inhibitors with a spirocyclic moiety. Authors: Adachi, K. / Manabe, T. / Yamasaki, T. / Suma, A. / Orita, T. / Furuzono, T. / Adachi, T. / Ohata, Y. / Akiyama, Y. / Miyazaki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zh4.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zh4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8zh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zh4_validation.pdf.gz | 822.6 KB | Display | wwPDB validaton report |
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Full document | 8zh4_full_validation.pdf.gz | 822.8 KB | Display | |
Data in XML | 8zh4_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 8zh4_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/8zh4 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/8zh4 | HTTPS FTP |
-Related structure data
Related structure data | 8zhaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18443.689 Da / Num. of mol.: 1 / Mutation: F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds | ||||||
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#2: Chemical | ChemComp-PG4 / | ||||||
#3: Chemical | ChemComp-A1L1V / ( Mass: 344.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32O3 | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 0.2M ammonium sulfate, 7% (w/v) PEG 8000, 5mM DTT, soaking the crystal with 1mM compound 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: MAR CCD 300 mm / Detector: CCD / Date: Sep 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→45.56 Å / Num. obs: 18381 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Rrim(I) all: 0.055 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.82→1.86 Å / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1077 / CC1/2: 0.885 / Rpim(I) all: 0.288 / Rrim(I) all: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→45.56 Å / SU ML: 0.1573 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4011 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→45.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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