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- PDB-8t5a: HIV-1 Integrase Catalytic Core Domain (CCD) F185H/Y99H/A128T Muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t5a | ||||||
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Title | HIV-1 Integrase Catalytic Core Domain (CCD) F185H/Y99H/A128T Mutant Complexed with STP03-0404 | ||||||
![]() | Integrase | ||||||
![]() | VIRAL PROTEIN / Integrase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dinh, T. / Kvaratskhelia, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. Authors: Dinh, T. / Tber, Z. / Rey, J.S. / Mengshetti, S. / Annamalai, A.S. / Haney, R. / Briganti, L. / Amblard, F. / Fuchs, J.R. / Cherepanov, P. / Kim, K. / Schinazi, R.F. / Perilla, J.R. / Kim, B. / Kvaratskhelia, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8t52C ![]() 8s9qS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16770.176 Da / Num. of mol.: 1 / Mutation: F185H, Y99H, A128T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-WBV / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M (NH4)2SO4, 0.1 M sodium cacodylate (pH = 6.5), 10% PEG 8000, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→45.28 Å / Num. obs: 10546 / % possible obs: 69.77 % / Redundancy: 2 % / Biso Wilson estimate: 25.2 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.08091 / Rpim(I) all: 0.08091 / Rrim(I) all: 0.1144 / Net I/σ(I): 7.97 |
Reflection shell | Resolution: 1.93→2.003 Å / Rmerge(I) obs: 0.3051 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 39 / CC1/2: 0.788 / CC star: 0.939 / Rpim(I) all: 0.3051 / Rrim(I) all: 0.3051 / % possible all: 2.63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8S9Q Resolution: 1.93→45.28 Å / SU ML: 0.2922 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7414 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→45.28 Å
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Refine LS restraints |
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LS refinement shell |
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