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- PDB-4ovl: Interrogating HIV integrase for compounds that bind- a SAMPL challenge -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ovl | ||||||
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Title | Interrogating HIV integrase for compounds that bind- a SAMPL challenge | ||||||
![]() | Integrase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() RNA stem-loop binding / : / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. | ||||||
![]() | ![]() Title: Interrogating HIV integrase for compounds that bind--a SAMPL challenge. Authors: Peat, T.S. / Dolezal, O. / Newman, J. / Mobley, D. / Deadman, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ce9C ![]() 4ceaC ![]() 4cebC ![]() 4cecC ![]() 4cedC ![]() 4ceeC ![]() 4cefC ![]() 4ceoC ![]() 4ceqC ![]() 4cerC ![]() 4cesC ![]() 4cezC ![]() 4cf0C ![]() 4cf1C ![]() 4cf2C ![]() 4cf8C ![]() 4cf9C ![]() 4cfaC ![]() 4cfbC ![]() 4cfcC ![]() 4cfdC ![]() 4cgdC ![]() 4cgfC ![]() 4cggC ![]() 4cghC ![]() 4cgiC ![]() 4cgjC ![]() 4chnC ![]() 4choC ![]() 4chpC ![]() 4chqC ![]() 4chyC ![]() 4chzC ![]() 4cieC ![]() 4cifC ![]() 4cigC ![]() 4cj3C ![]() 4cj4C ![]() 4cj5C ![]() 4cjeC ![]() 4cjfC ![]() 4cjkC ![]() 4cjlC ![]() 4cjpC ![]() 4cjqC ![]() 4cjrC ![]() 4cjsC ![]() 4cjtC ![]() 4cjuC ![]() 4cjvC ![]() 4cjwC ![]() 4ck1C ![]() 4ck2C ![]() 4ck3C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 57 - 209 / Label seq-ID: 28 - 180
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 20044.672 Da / Num. of mol.: 2 / Mutation: C56S, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q76353, UniProt: P12497*PLUS, ![]() |
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-Non-polymers , 6 types, 154 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/1TD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/1TD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-ACY / ![]() #4: Chemical | #5: Chemical | ChemComp-GOL / | ![]() #6: Chemical | ChemComp-EDO / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 mM TRIS PH 8.0, 250 mM NACL, 30 mM MGCL2, 5 mM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 mM SODIUM ACETATE BUFFER PH 5.0 TO 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→45.6 Å / Num. obs: 42336 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2 / Num. measured obs: 6138 |
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Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.766 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→45.62 Å
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Refine LS restraints |
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