[English] 日本語
![](img/lk-miru.gif)
- PDB-2qnq: HIV-1 Protease in complex with a chloro decorated pyrrolidine-bas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qnq | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 Protease in complex with a chloro decorated pyrrolidine-based inhibitor | ||||||
![]() | Gag-Pol polyprotein (Pr160Gag-Pol) | ||||||
![]() | HYDROLASE / protein-ligand complex / AIDS / Aspartyl protease / Capsid maturation / Core protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Phosphorylation / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
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, J. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 917.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 919.5 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pqzSC ![]() 2pwcC ![]() 2pwrC ![]() 2qnnC ![]() 2qnpC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV-1 retropepsin Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-QN3 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.8M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 10478 / Num. obs: 10478 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 11 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.27 / Num. unique all: 665 / Rsym value: 25.2 / % possible all: 93.9 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 2PQZ Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
|