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- PDB-5yrs: X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrah... -
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Basic information
Entry | Database: PDB / ID: 5yrs | |||||||||
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Title | X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Its SIHB with Catalytic Aspartate | |||||||||
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![]() | HYDROLASE / HIV-1 PROTEASE / TETRAHEDRAL INTERMEDIATE / SHORT IONIC HYDROGEN BOND / SUBSTRATE COMPLEX / RT-RH | |||||||||
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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / 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 | ![]() ![]() ![]() | |||||||||
![]() | Das, A. / Mahale, S. / Prashar, V. / Bihani, S. / Ferrer, J.-L. / Hosur, M.V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate. Authors: Das, A. / Mahale, S. / Prashar, V. / Bihani, S. / Ferrer, J.L. / Hosur, M.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lv1S S: Starting model for refinement |
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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
#1: Protein | Mass: 11163.094 Da / Num. of mol.: 1 / Mutation: C95M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11102.976 Da / Num. of mol.: 1 / Mutation: C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 774.815 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THIS SEQUENCE CORRESPONDS TO RT-RH CLEAVAGE SITE, NATURALLY OCCURING IN HIV-1 GAG-POL POLYPROTEIN. Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
Sequence details | THE AUTHOR STATES THAT RESIDUE HPH X 4 IS L-PHENYLALANINE AND HYDRATED L-PHE RESIDUE HAVING ...THE AUTHOR STATES THAT RESIDUE HPH X 4 IS L-PHENYLALAN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M PHOSPHATE-0.2M CITRATE BUFFER, AMM. SULPHATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2008 |
Radiation | Monochromator: A HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 17226 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.76 |
Reflection shell | Resolution: 1.76→1.81 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.98 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LV1 Resolution: 1.76→50 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: 1 / Resolution: 1.76→50 Å
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Refine LS restraints |
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