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Yorodumi- PDB-1z8c: Crystal structure of the complex of mutant HIV-1 protease (l63P, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z8c | ||||||
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Title | Crystal structure of the complex of mutant HIV-1 protease (l63P, A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-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 HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Duskova, J. / Skalova, T. / Dohnalek, J. / Petrokova, H. / Hasek, J. | ||||||
Citation | Journal: To be Published Title: Mutational Study of Pseudopeptide Inhibitor Binding to HIV-1 Protease; Analysis of Four X-ray Structures Authors: Duskova, J. / Skalova, T. / Dohnalek, J. / Petrokova, H. / Hasek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z8c.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z8c.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/1z8c ftp://data.pdbj.org/pub/pdb/validation_reports/z8/1z8c | HTTPS FTP |
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-Related structure data
Related structure data | 1zbgC 1zpkC 1sp5S 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 | dimer in asymmetric unit is biological assembly |
-Components
#1: Protein | Mass: 10879.831 Da / Num. of mol.: 2 / Mutation: L63P, A71V, V82T, I84V 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(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P03367, UniProt: Q9JAU9*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-0ZS / | #3: Chemical | ChemComp-SO4 / | #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: 2.02 Å3/Da / Density % sol: 39.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2M ammonium sulphate, 5% polyethylene glycol 400, 1M natrium MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 2002 / Details: mirrors XOS Nonius |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28 Å / Num. all: 9810 / Num. obs: 9225 / % possible obs: 94 % / Observed criterion σ(I): -9999 / Redundancy: 3 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.9 / Num. unique all: 626 / Rsym value: 0.412 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SP5 Resolution: 2.2→28 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: used maximum likelihood procedure
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Displacement parameters | Biso mean: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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