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- PDB-3avb: Crystal structures of novel allosteric peptide inhibitors of HIV ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3avb | ||||||
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Title | Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site | ||||||
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![]() | RECOMBINATION/INHIBITOR / ![]() ![]() | ||||||
Function / homology | ![]() : / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. / Deadman, J.J. / Newman, J. / Rhodes, D.I. | ||||||
![]() | ![]() Title: Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site. Authors: Rhodes, D.I. / Peat, T.S. / Vandegraaff, N. / Jeevarajah, D. / Newman, J. / Martyn, J. / Coates, J.A. / Ede, N.J. / Rea, P. / 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 | ![]() | 80.9 KB | Display | ![]() |
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PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3av9C ![]() 3avaC ![]() 3avcC ![]() 3avfC ![]() 3avgC ![]() 3avhC ![]() 3aviC ![]() 3avjC ![]() 3avkC ![]() 3avlC ![]() 3avmC ![]() 3avnC 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 / Protein/peptide , 2 types, 4 molecules ABXY
#1: Protein | ![]() Mass: 20044.672 Da / Num. of mol.: 2 / Fragment: CCD domain (UNP RESIDUES 1197-1359) / Mutation: C56S, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | |
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-Non-polymers , 4 types, 163 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K PH range: 5.0-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→61.4 Å / Num. all: 32210 / Num. obs: 32210 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.97 Å2 / Biso mean: 24.6276 Å2 / Biso min: 3.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→45.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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