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Yorodumi- PDB-3nuj: Crystal Structure of HIV-1 Protease Mutant I54V with Antiviral Dr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nuj | ||||||
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Title | Crystal Structure of HIV-1 Protease Mutant I54V with Antiviral Drug Amprenavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / enzyme inhibition / aspartic protease / HIV/AIDS / conformational change / Amprenavir / 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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / AB INITIO / Resolution: 1.5 Å | ||||||
Authors | Shen, C.H. / 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 | 3nuj.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nuj.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nuj_validation.pdf.gz | 817.6 KB | Display | wwPDB validaton report |
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Full document | 3nuj_full_validation.pdf.gz | 819.1 KB | Display | |
Data in XML | 3nuj_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3nuj_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/3nuj ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3nuj | HTTPS FTP |
-Related structure data
Related structure data | 3nu3C 3nu4C 3nu5C 3nu6C 3nu9C 3nuoC 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: 10726.649 Da / Num. of mol.: 2 / Fragment: residues 501-599 / Mutation: Q7K, L33I, I54V, 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-IOD / #3: Chemical | ChemComp-478 / { | #4: 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: 2.65 Å3/Da / Density % sol: 53.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 5.4 with 0.13M NaCl, 0.1M NaOAc. The inhibitor was mixed with ...Details: Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 5.4 with 0.13M NaCl, 0.1M NaOAc. The inhibitor was mixed with protease in a ratio 5:1, 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: Nov 8, 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: 1.5→50 Å / Num. all: 37222 / Num. obs: 37222 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.5→10 Å / Num. parameters: 15872 / Num. restraintsaints: 20347 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 1634 / Occupancy sum non hydrogen: 1664.55 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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