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Yorodumi- PDB-1z1r: HIV-1 protease complexed with Macrocyclic peptidomimetic inhibitor 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z1r | |||||||||
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Title | HIV-1 protease complexed with Macrocyclic peptidomimetic inhibitor 2 | |||||||||
Components | Pol polyprotein | |||||||||
Keywords | HYDROLASE / macrocyclic inhibitors / peptidomimetic inhibitors / HIV1 protease | |||||||||
Function / homology | Function and homology information 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 ...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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å | |||||||||
Authors | Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. ...Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. / Reid, R.C. / Fairlie, D.P. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease Authors: Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. / Reid, R.C. / Fairlie, D.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z1r.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z1r.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 1z1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z1r_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1z1r_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1z1r_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1z1r_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/1z1r ftp://data.pdbj.org/pub/pdb/validation_reports/z1/1z1r | HTTPS FTP |
-Related structure data
Related structure data | 1b6jC 1b6kC 1b6lC 1b6mC 1b6pC 1z1hC 1b6o 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 | the biological unit is a homodimer. The two molecules in the asymmetric unit represent the biological assembly |
-Components
#1: Protein | Mass: 10765.687 Da / Num. of mol.: 2 / Fragment: HIV-1 protease / Mutation: Gln7Lys Leu33Ile Cys67Aba Cys95Aba / Source method: obtained synthetically Details: chemically synthesised by solid phase peptide synthesis References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-HBH / | #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: 1.96 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30-60% ammonium sulfate, 0.1M acetate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: Yale mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 14904 / Num. obs: 14904 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.073 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.295 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1B6O 1b6o Resolution: 1.85→8 Å Isotropic thermal model: anisotropic, with bulk solvent correction Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å
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