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Yorodumi- PDB-3ebz: High Resolution HIV-2 Protease Structure in Complex with Clinical... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ebz | ||||||
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Title | High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / HIV-2 / aspartic protease / inhibitor / protease-drug complex | ||||||
Function / homology | Function and homology information HIV-2 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 ...HIV-2 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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 type 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kovalevsky, A.Y. / Weber, I.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease Authors: Kovalevsky, A.Y. / Louis, J.M. / Aniana, A. / Ghosh, A.K. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ebz.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebz.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ebz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebz ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebz | HTTPS FTP |
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-Related structure data
Related structure data | 3ec0C 3ecgC 2ienS 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10728.337 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 2 (ISOLATE ROD) Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04584, HIV-2 retropepsin |
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-Non-polymers , 6 types, 235 molecules
#2: Chemical | ChemComp-IMD / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-017 / ( | #7: 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: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 0.6-0.7M imidazole, 0.12-0.14M Zn(OAc)2 buffer, 1.25-2M NaCl, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2006 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→10 Å / Num. all: 51581 / Num. obs: 42711 / % possible obs: 83 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / Num. unique all: 3445 / Rsym value: 0.29 / % possible all: 61.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IEN Resolution: 1.2→10 Å / Num. parameters: 16744 / Num. restraintsaints: 21002 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
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Displacement parameters | Biso mean: 22.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 1556 / Occupancy sum non hydrogen: 1764.75 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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