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- PDB-3vq8: HIV-1 IN core domain in complex with (3R)-3,4-dihydro-2H-chromen-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vq8 | ||||||
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Title | HIV-1 IN core domain in complex with (3R)-3,4-dihydro-2H-chromen-3-ylmethanol | ||||||
![]() | POL polyprotein | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / RNaseH / DNA binding / DNA cleavage / DNA integration / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wielens, J. / Chalmers, D.K. / Parker, M.W. / Scanlon, M.J. | ||||||
![]() | ![]() Title: Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? Authors: Wielens, J. / Headey, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.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 | ![]() | 70.5 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vq4C ![]() 3vq5C ![]() 3vq6C ![]() 3vq7C ![]() 3vq9C ![]() 3vqaC ![]() 3vqbC ![]() 3vqcC ![]() 3vqdC ![]() 3vqeC ![]() 3vqpC ![]() 3vqqC ![]() 4ah9C ![]() 4ahrC ![]() 4ahsC ![]() 4ahtC ![]() 4ahuC ![]() 4ahvC ![]() 3l3uS S: Starting model for refinement 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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17101.393 Da / Num. of mol.: 2 / Fragment: integrase core domain, UNP residues 771-927 / Mutation: C56S, S123G, T124A, K127R, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 80 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6M AmSO4, 0.1M Na Citrate pH 4.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 15, 2009 / Details: mirror |
Radiation | Monochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9544 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. all: 50498 / Num. obs: 47885 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.119 / Rsym value: 0.081 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 1.44→1.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7027 / Rsym value: 0.706 / % possible all: 85.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3l3u Resolution: 1.6→26.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.877 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.344 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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