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Yorodumi- PDB-1qs4: Core domain of HIV-1 integrase complexed with Mg++ and 1-(5-chlor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qs4 | ||||||
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Title | Core domain of HIV-1 integrase complexed with Mg++ and 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone | ||||||
Components | PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49)) | ||||||
Keywords | TRANSFERASE / DNA INTEGRATION / INTEGRASE / HIV / ASPARTYL PROTEASE / ENDONUCLEASE | ||||||
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 / endonuclease activity / 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 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Goldgur, Y. / Craigie, R. / Fujiwara, T. / Yoshinaga, T. / Davies, D.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Authors: Goldgur, Y. / Craigie, R. / Cohen, G.H. / Fujiwara, T. / Yoshinaga, T. / Fujishita, T. / Sugimoto, H. / Endo, T. / Murai, H. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qs4.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qs4.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qs4_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 1qs4_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 1qs4_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1qs4_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qs4 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qs4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16813.219 Da / Num. of mol.: 3 / Fragment: Catalytic core domain / Mutation: F185K, W131E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q76353, UniProt: P12497*PLUS, RNA-directed DNA polymerase #2: Chemical | #3: Chemical | ChemComp-100 / | #4: 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: 2.4 Å3/Da / Density % sol: 48.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 30% PEG 4000, 100 MM HEPES, 5 MM MGCL2, 5 MM DTT, 1% GLYCEROL, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging dropDetails: Goldgur, Y., (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 9150. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.07 Å / Num. obs: 26564 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.12 % / Biso Wilson estimate: 29.64 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.274 / % possible all: 81.2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Observed criterion σ(I): -3 |
Reflection shell | *PLUS % possible obs: 81 % / Mean I/σ(I) obs: 2.86 |
-Processing
Software |
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Refinement | Resolution: 2.1→38.07 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET'S PRINCIPLE / Bsol: 73.9058 Å2 / ksol: 0.3627 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→38.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.13 Å / Total num. of bins used: 25
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / % reflection Rfree: 5 % |