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Yorodumi- PDB-1izh: Inhibitor of HIV protease with unusual binding mode potently inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1izh | ||||||
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Title | Inhibitor of HIV protease with unusual binding mode potently inhibiting multi-resistant protease mutants | ||||||
Components | proteinaseProtease | ||||||
Keywords | HYDROLASE / HIV-1 proteinase / potent inhibitor / subsite binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. ...Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / Vondrasek, J. / Klimkait, T. / Kraeusslich, H.-G. / Hilgenfeld, R. / Konvalinka, J. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2002 Title: Unusual Binding Mode of an HIV-1 Protease Inhibitor Explains its Potency against Multi-drug-resistant Virus Strains Authors: Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / ...Authors: Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / Vondrasek, J. / Klimkait, T. / Kraeusslich, H.-G. / Hilgenfeld, R. / Konvalinka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1izh.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1izh.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 1izh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/1izh ftp://data.pdbj.org/pub/pdb/validation_reports/iz/1izh | HTTPS FTP |
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-Related structure data
Related structure data | 1iziC 5hvpS C: citing same article (ref.) 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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Details | The biological assembly is the homodimer as found in the asymmetric unit |
-Components
#1: Protein | Mass: 10830.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q90EB9, HIV-1 retropepsin #2: Chemical | ChemComp-Q50 / {( | #3: 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: 2.7 Å3/Da / Density % sol: 54.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, DTT, EDTA, NaN3, KCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 18388 / Num. obs: 18388 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.74 % / Biso Wilson estimate: 22.772 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3 / Num. unique all: 1715 / % possible all: 91.3 |
Reflection | *PLUS Highest resolution: 1.9 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 5HVP Resolution: 1.9→43.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.312 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.734 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→43.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |