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Open data
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Basic information
Entry | Database: PDB / ID: 3jvy | ||||||
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Title | HIV-1 Protease Mutant G86A with DARUNAVIR | ||||||
![]() | Gag-Pol polyprotein | ||||||
![]() | HYDROLASE / HIV-1 Protease / Mutant G86A / INHIBITOR / DARUNAVIR / AIDS / Aspartyl protease / METAL-BINDING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tie, Y. / Weber, I.T. | ||||||
![]() | ![]() Title: Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV-1 protease Authors: Ishima, R. / Gong, Q. / Tie, Y. / Weber, I.T. / Louis, J.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jvwC ![]() 3jw2C ![]() 2ienS 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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Details | dimer |
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Components
#1: Protein | Mass: 10754.702 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, L63I, C67A, G86A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol, Human immunodeficiency virus type 1 / Plasmid: pET11a / Production host: ![]() ![]() #2: Chemical | ChemComp-NA / | #3: Chemical | #4: Chemical | ChemComp-017 / ( | #5: 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: 54.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Crystallization drops contained 1 ul protein and 1.6 ul of the reservoir solution of 8% SODIUM CHLORIDE, MES PH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2005 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. all: 31701 / Num. obs: 31701 / % possible obs: 95.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.7 | |||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.474 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2IEN Resolution: 1.6→10 Å / Num. parameters: 16244 / Num. restraintsaints: 21444 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1657.83 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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