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Yorodumi- PDB-3qaa: HIV-1 wild type protease with a substituted bis-Tetrahydrofuran i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qaa | ||||||
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Title | HIV-1 wild type protease with a substituted bis-Tetrahydrofuran inhibitor, GRL-044-10A | ||||||
Components | HIV-1 Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / aspartic acid protease / HIV-1 protease inhibitor GRL-044-10A / substituted bis-tetrahydrofuran inhibitor / wild-type HIV-1 protease / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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: 1.4 Å | ||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2011 Title: Design of substituted bis-Tetrahydrofuran (bis-THF)-derived Potent HIV-1 Protease Inhibitors, Protein-ligand X-ray Structure, and Convenient Syntheses of bis-THF and Substituted bis-THF Ligands. Authors: Ghosh, A.K. / Martyr, C.D. / Steffey, M. / Wang, Y.F. / Agniswamy, J. / Amano, M. / Weber, I.T. / Mitsuya, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qaa.cif.gz | 106.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qaa.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 3qaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qaa_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3qaa_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3qaa_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3qaa_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/3qaa ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qaa | HTTPS FTP |
-Related structure data
Related structure data | 2qciS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: residues 501-599 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P03366, HIV-1 retropepsin |
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-Non-polymers , 5 types, 140 molecules
#2: Chemical | ChemComp-G04 / ( | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, 0.1 M Sodium Citrate, 1.2 M Sodium Chloride, 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 / Wavelength: 0.8 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 45049 / Num. obs: 45049 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.1 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCI Resolution: 1.4→10 Å / Num. parameters: 16753 / Num. restraintsaints: 22762 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: conjugage gradient minimization
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Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1658.05 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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