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Yorodumi- PDB-6we7: HIV Integrase core domain in complex with inhibitor 3-methyl-2-{5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6we7 | ||||||
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Title | HIV Integrase core domain in complex with inhibitor 3-methyl-2-{5-methyl-2-[2-(thiophen-2-yl)ethynyl]-1- benzofuran-3-yl}butanoic acid | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å | ||||||
Authors | Gorman, M.A. / Parker, M.W. | ||||||
Citation | Journal: To Be Published Title: HIV Integrase core domain in complex with inhibitor Authors: Gorman, M.A. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6we7.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6we7.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 6we7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6we7 ftp://data.pdbj.org/pub/pdb/validation_reports/we/6we7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18048.494 Da / Num. of mol.: 1 / Fragment: UNP residues 50-212 / Mutation: Q53E,C56S,G124S,A125T,W131E,V151I,F185K,Q209E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: F2WR52, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-TXM / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.48 % / Description: Bi-pyramid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 100 mM potassium iodide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→46.74 Å / Num. obs: 7524 / % possible obs: 99.7 % / Redundancy: 16.5 % / Biso Wilson estimate: 31.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.02 / Rrim(I) all: 0.082 / Χ2: 1.01 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.28→2.35 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 652 / CC1/2: 0.948 / Rpim(I) all: 0.174 / Rrim(I) all: 0.724 / Χ2: 1.04 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.28→43.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 14.235 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.282 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.389 Å2
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Refinement step | Cycle: 1 / Resolution: 2.28→43.8 Å
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Refine LS restraints |
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