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- PDB-2pwr: HIV-1 protease in complex with a carbamoyl decorated pyrrolidine-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pwr | ||||||
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Title | HIV-1 protease in complex with a carbamoyl decorated pyrrolidine-based inhibitor | ||||||
![]() | Gag-Pol polyprotein (Pr160Gag-Pol) | ||||||
![]() | HYDROLASE / protein-ligand complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boettcher, B. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
![]() | ![]() Title: Structure-Guided Design of C2-Symmetric HIV-1 Protease Inhibitors Based on a Pyrrolidine Scaffold. Authors: Blum, A. / Bottcher, J. / Heine, A. / Klebe, G. / Diederich, W.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
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PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 794.3 KB | Display | ![]() |
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Full document | ![]() | 797.2 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pqzSC ![]() 2pwcC ![]() 2qnnC ![]() 2qnpC ![]() 2qnqC C: citing same article ( 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-G4G / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.25M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2006 / Details: mirrors |
Radiation | Monochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. all: 33531 / Num. obs: 33531 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.56 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 34.15 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.59 / Num. unique all: 1687 / Rsym value: 0.23 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2PQZ Resolution: 1.5→10 Å / Num. parameters: 7025 / Num. restraintsaints: 6438 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 1590 / Occupancy sum non hydrogen: 1742.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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