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- PDB-1iiq: CRYSTAL STRUCTURE OF HIV-1 PROTEASE COMPLEXED WITH A HYDROXYETHYL... -
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Basic information
Entry | Database: PDB / ID: 1iiq | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-1 PROTEASE COMPLEXED WITH A HYDROXYETHYLAMINE PEPTIDOMIMETIC INHIBITOR | ||||||
![]() | PROTEASE RETROPEPSIN | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV protease / peptidomimetics / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M. | ||||||
![]() | ![]() Title: Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a ...Title: Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a peptidomimetic inhibitor. Authors: Dohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M. #1: ![]() Title: A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease Authors: Dohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1hsgS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-0ZR / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: ammonium phosphate, sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 280K |
Crystal grow | *PLUS Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409., Dohnalek, J., (1998) Gen. Physiol. Biophys., 17, Suppl. 1, 9., Buchtelova, E., (1999) Mater. Struct., 6, 6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.83→11 Å / Num. all: 20474 / Num. obs: 20474 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.83→1.88 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1382 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 188100 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 93.7 % / Num. measured obs: 1392 / Rmerge(I) obs: 0.22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HSG Resolution: 1.83→10.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1339622.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: Engh & Huber, ligand parametrisation: CSD structural database Details: Used maximum likelihood and conjugated gradient least squares refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 87.55 Å2 / ksol: 0.471 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→10.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.226 / Rfactor Rwork: 0.177 |