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Yorodumi- PDB-1zpk: Crystal structure of the complex of mutant HIV-1 protease (A71V, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zpk | ||||||
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Title | Crystal structure of the complex of mutant HIV-1 protease (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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 1zpk.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zpk.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zpk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1zpk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1zpk_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1zpk_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/1zpk ftp://data.pdbj.org/pub/pdb/validation_reports/zp/1zpk | HTTPS FTP |
-Related structure data
Related structure data | 1z8cC 1zbgC 1a9mS 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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-Components
#1: Protein | Mass: 10895.874 Da / Num. of mol.: 2 / Mutation: 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: Q7ZCL6*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-0ZS / | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 0ZS 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: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 298 K / Method: microseeding / pH: 4.4 Details: 0.5 M NaCl, 0.1 M Na Citrate, 10% Glycerol, pH 4.4, microseeding, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2000 / Details: microfocusing mirrors - testing |
Radiation | Monochromator: Diamond C 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 21955 / Num. obs: 21955 / % possible obs: 99.9 % / Observed criterion σ(I): -999 / Redundancy: 6.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 48.4 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1464 / Rsym value: 0.37 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A9M Resolution: 1.65→10 Å / Num. parameters: 16137 / Num. restraintsaints: 20476 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.13 Å / Num. disordered residues: 21 / Occupancy sum hydrogen: 1645 / Occupancy sum non hydrogen: 1701.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å /
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