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- PDB-7sia: HIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sia | ||||||
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Title | HIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(4-{2-[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)formamido]ethyl}piperazin-1-yl)methyl]phenyl}ethynyl)-5-methyl-1-benzofuran-3-yl]acetic acid | ||||||
![]() | Integrase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() RNA-directed DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gorman, M.A. / Parker, M.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.1 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 672.5 KB | Display | ![]() |
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Full document | ![]() | 683.4 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w0uC ![]() 6wc8C ![]() 6we7C ![]() 7l1pC ![]() 7l2yC ![]() 7rq0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17655.059 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 50-212) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76353, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | ChemComp-9I4 / ( | #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % / Description: Bi-pyamind |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.33 Å / Num. obs: 47732 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 1.08 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1392 / CC1/2: 0.828 / Rpim(I) all: 0.307 / Rrim(I) all: 0.812 / Χ2: 0.97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7RQ0 Resolution: 1.85→46.28 Å / Cross valid method: THROUGHOUT / σ(F): 7.62 / Phase error: 35.54 / Stereochemistry target values: TWIN_LSQ_F / Details: TLS, Anomalous, Individual isotropic B factors
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→46.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.1266 Å / Origin y: 12.0226 Å / Origin z: -18.4032 Å
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Refinement TLS group | Selection details: all |