[English] 日本語
![](img/lk-miru.gif)
- PDB-3ecg: High Resolution HIV-2 Protease Structure in Complex with Antivira... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ecg | ||||||
---|---|---|---|---|---|---|---|
Title | High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065 | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE / HIV-2 / aspartic protease / inhibitor / protease-inhibitor complex | ||||||
Function / homology | ![]() HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kovalevsky, A.Y. / Weber, I.T. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 811.7 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ebzC ![]() 3ec0C ![]() 2ienS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
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.) ![]() Plasmid: pET11a / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 231 molecules ![](data/chem/img/065.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-065 / ( | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 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: 1.18→10 Å / Num. all: 51263 / Num. obs: 40772 / % possible obs: 79.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.18→1.22 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3063 / % possible all: 52.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2IEN Resolution: 1.18→10 Å / Num. parameters: 16672 / Num. restraintsaints: 20855 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
| |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.8 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 1556 / Occupancy sum non hydrogen: 1764.85 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|