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Yorodumi- PDB-6vlh: HIV Integrase Core domain (IN) in complex with dimer-spanning ligand -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vlh | ||||||
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Title | HIV Integrase Core domain (IN) in complex with dimer-spanning ligand | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE / Virus / Inhibitor / Complex / HIV Integrase | ||||||
Function / homology | Function and homology information DNA integration / RNA stem-loop binding / 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: 2.036 Å | ||||||
Authors | Gorman, M.A. / Parker, M.W. | ||||||
Citation | Journal: To Be Published Title: HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor Authors: Scanlon, M. / Gorman, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vlh.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vlh.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vlh_validation.pdf.gz | 667.2 KB | Display | wwPDB validaton report |
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Full document | 6vlh_full_validation.pdf.gz | 679.8 KB | Display | |
Data in XML | 6vlh_validation.xml.gz | 15 KB | Display | |
Data in CIF | 6vlh_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vlh ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vlh | HTTPS FTP |
-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: 17872.305 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 50-211) / 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: F2WR39, RNA-directed DNA polymerase #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-R2A / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.8 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: MX2 / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.036→46.38 Å / Num. obs: 18621 / % possible obs: 99.3 % / Redundancy: 8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.021 / Rrim(I) all: 0.059 / Χ2: 1.06 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.036→2.09 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1287 / Rpim(I) all: 0.172 / Rrim(I) all: 0.472 / Χ2: 1.2 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.036→46.306 Å / Cross valid method: THROUGHOUT / σ(F): 8.54 / Phase error: 37.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.036→46.306 Å
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Refine LS restraints |
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LS refinement shell |
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