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Yorodumi- PDB-2r43: I50V HIV-1 protease in complex with an amino decorated pyrrolidin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r43 | ||||||
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Title | I50V HIV-1 protease in complex with an amino decorated pyrrolidine-based inhibitor | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / protein-ligand complex | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Boettcher, J. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural and Kinetic Analysis of Pyrrolidine-Based Inhibitors of the Drug-Resistant Ile84Val Mutant of HIV-1 Protease Authors: Bottcher, J. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r43.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r43.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2r43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/2r43 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r43 | HTTPS FTP |
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-Related structure data
Related structure data | 2r38C 2r3tC 2r3wC 2pwcS 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
#1: Protein | Mass: 10789.729 Da / Num. of mol.: 2 / Mutation: I50V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: gag-pol / Gene: pol / Plasmid: peT11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3)pLysS References: UniProt: Q5RZ08, UniProt: P03367*PLUS, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-G3G / | #5: 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: 2.667951 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.5M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97803 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2007 Details: Double crystal monochromator with two sets of mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97803 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→25 Å / Num. obs: 31985 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1463 / Rsym value: 0.375 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PWC Resolution: 1.58→10 Å / Num. parameters: 6825 / Num. restraintsaints: 6359 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 1581 / Occupancy sum non hydrogen: 1696.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→10 Å
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Refine LS restraints |
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