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Yorodumi- PDB-1zsr: Crystal structure of wild type HIV-1 protease (BRU isolate) with ... -
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-Basic information
Entry | Database: PDB / ID: 1zsr | ||||||
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Title | Crystal structure of wild type HIV-1 protease (BRU isolate) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2 | ||||||
Components | PROTEASE RETROPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / PROTEASE / PEPTIDOMIMETIC INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 activation of host apoptosis / HIV-1 retropepsin / 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 / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Skalova, T. / Dohnalek, J. / Duskova, J. / Petrokova, H. / Hasek, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 A resolution. Authors: Duskova, J. / Dohnalek, J. / Skalova, T. / Petrokova, H. / Vondrackova, E. / Hradilek, M. / Konvalinka, J. / Soucek, M. / Brynda, J. / Fabry, M. / Sedlacek, J. / Hasek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zsr.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zsr.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zsr_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1zsr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1zsr_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1zsr_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/1zsr ftp://data.pdbj.org/pub/pdb/validation_reports/zs/1zsr | HTTPS FTP |
-Related structure data
Related structure data | 1zsfC 1iiqS 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: 10819.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pT7Q10H1N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P03367, UniProt: P03366*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-0ZT / | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 0ZT IS A PSEUDOPEPT | |
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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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 1 M Ammonium Phosphate, 0.1 M Na Citrate, 3 mg/ml protein, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1997 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→40 Å / Num. all: 10981 / Num. obs: 10981 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -999 / Redundancy: 6.98 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.06→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.98 / Num. unique all: 553 / Rsym value: 0.305 / % possible all: 69.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IIQ Resolution: 2.06→40 Å / Isotropic thermal model: Isotropic / Cross valid method: R-FREE statistic throughout / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used maximum likelihood refinement procedure against F values. The classical crystallographic residual used as target function in the final refinement cycle.
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Solvent computation | Solvent model: Jiang & Brunger, 1994 / Bsol: 101.4 Å2 / ksol: 0.396 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.253 Å / Luzzati d res low obs: 6 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.15 Å
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