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Yorodumi- PDB-3nu4: Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Dr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nu4 | ||||||
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Title | Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Drug Amprenavir | ||||||
Components | protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / enzyme inhibition / aspartic protease / HIV/AIDS / conformational change / Amprenavir / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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 / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Wang, Y.-F. / Kovalevsky, A.Y. / Weber, I.T. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. Authors: Shen, C.H. / Wang, Y.F. / Kovalevsky, A.Y. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nu4.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nu4.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 3nu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/3nu4 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3nu4 | HTTPS FTP |
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-Related structure data
Related structure data | 3nu3SC 3nu5C 3nu6C 3nu9C 3nujC 3nuoC S: Starting model for refinement C: citing same article (ref.) |
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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: 10754.703 Da / Num. of mol.: 2 / Fragment: residues 501-599 / Mutation: Q7K, V32I, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag, pol / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | ChemComp-NA / | #3: Chemical | #4: Chemical | ChemComp-478 / { | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: The vapour diffusion, hanging drop method is applied. Amprenvir was dissolved in DMSO. Protein concentration is 2.2 mg/ml. The ratio of inhibitor to protein is 5:1 in 0.1 M sodium acetate ...Details: The vapour diffusion, hanging drop method is applied. Amprenvir was dissolved in DMSO. Protein concentration is 2.2 mg/ml. The ratio of inhibitor to protein is 5:1 in 0.1 M sodium acetate buffer (ph=5.4), with 0.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 66626 / Num. obs: 66626 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.517 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4482 / % possible all: 62.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.2→10 Å / Num. parameters: 15883 / Num. restraintsaints: 20162 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: conjugate gradient minimization
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Refine analyze | Num. disordered residues: 15 / Occupancy sum hydrogen: 1637 / Occupancy sum non hydrogen: 1674.81 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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