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- PDB-2qd8: HIV-1 Protease Mutant I84V with potent Antiviral inhibitor GRL-98065 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qd8 | ||||||
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Title | HIV-1 Protease Mutant I84V with potent Antiviral inhibitor GRL-98065 | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE / HIV-1 protease mutant I84V / protease inhibitor | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() Title: Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. Authors: Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 83.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qciC ![]() 2qd6C ![]() 2qd7C ![]() 2z4oSC 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: 10726.650 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A, I84V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 230 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/065.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/065.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-065 / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25mM sodium acetate, 8% (w/v) sodium chloride, 10% (v/v) dimethylsulfoxide (DMSO), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2002 | |||||||||
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.35→50 Å / Num. all: 52465 / Num. obs: 51903 / % possible obs: 98.5 % / Redundancy: 9.8 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.3 | |||||||||
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.65 / Num. unique all: 4430 / % possible all: 86.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Z4O Resolution: 1.35→10 Å / Num. parameters: 17554 / Num. restraintsaints: 22821 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 1627 / Occupancy sum non hydrogen: 1742.69 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→10 Å
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Refine LS restraints |
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