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Yorodumi- PDB-5yrs: X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrah... -
+Open data
-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 | |||||||||
Components |
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Keywords | HYDROLASE / HIV-1 PROTEASE / TETRAHEDRAL INTERMEDIATE / SHORT IONIC HYDROGEN BOND / SUBSTRATE COMPLEX / RT-RH | |||||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | |||||||||
Authors | Das, A. / Mahale, S. / Prashar, V. / Bihani, S. / Ferrer, J.-L. / Hosur, M.V. | |||||||||
Funding support | India, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yrs.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yrs.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yrs ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yrs | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Human immunodeficiency virus 1 / Strain: M:B_HXB2R / Gene: gag-pol, HIV-1 PR B / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin |
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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.) Human immunodeficiency virus 1 / Strain: M:B_HXB2R / Gene: gag-pol, HIV-1 PR B / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin |
#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.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.987 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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