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- PDB-5eu7: Crystal structure of HIV-1 integrase catalytic core in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eu7 | ||||||
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Title | Crystal structure of HIV-1 integrase catalytic core in complex with Fab | ||||||
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![]() | VIRAL PROTEIN / Integrase / FAB / HIV | ||||||
Function / homology | ![]() integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Galilee, M. / Griner, S.L. / Stroud, R.M. / Alian, A. | ||||||
![]() | ![]() Title: The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Authors: Galilee, M. / Britan-Rosich, E. / Griner, S.L. / Uysal, S. / Baumgartel, V. / Lamb, D.C. / Kossiakoff, A.A. / Kotler, M. / Stroud, R.M. / Marx, A. / Alian, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.1 KB | Display | ![]() |
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PDB format | ![]() | 188.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 16710.076 Da / Num. of mol.: 2 / Fragment: Catalytic Core Domain, UNP residues 36-188 / Mutation: F185K, W131D Source method: isolated from a genetically manipulated source Details: Integrase Central Core Domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Antibody | Mass: 24927.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23273.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 100mM BisTrisPropane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→95.84 Å / Num. obs: 42891 / % possible obs: 98.7 % / Redundancy: 7.53 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.54 |
Reflection shell | Resolution: 2.64→2.729 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 5.92 / % possible all: 92.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EX4 and 1FVD Resolution: 2.64→95.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.094 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 1.18 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 42.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→95.84 Å
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Refine LS restraints |
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