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Yorodumi- PDB-1zbg: Crystal structure of a complex of mutant hiv-1 protease (A71V, V8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbg | ||||||
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Title | Crystal structure of a 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 / : / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 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 | 1zbg.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbg.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbg ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbg | HTTPS FTP |
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-Related structure data
Related structure data | 1z8cC 1zpkC 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 on special symmetry positions |
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Details | dimer in asymmetric unit is biological assembly |
-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 | #3: Chemical | ChemComp-0ZS / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 0ZS IS A PSEUDOPEPTIDE WITH THE HYDROXYETHYAMINE ISOSTERE IN THE R CONFIGURATION. THE ...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: 2.35 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 0.1 M Na Citrate, 1M NaCl, pH 4.4, VAPOR DIFFUSION, HANGING DROP, 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: microfocussing 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: 1.995→25 Å / Num. all: 16342 / Num. obs: 14316 / % possible obs: 87.6 % / Observed criterion σ(I): -999 / Redundancy: 3.2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.995→2.047 Å / Redundancy: 3 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.9 / Num. unique all: 997 / Rsym value: 0.325 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A9M Resolution: 1.995→25 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 3.217 / SU ML: 0.089 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 Stereochemistry target values: CCP4-5.0.2 Refmac5 dictionary Details: Used weighted maximum likelihood procedure.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.629 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.995→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.047 Å / Total num. of bins used: 20
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