[English] 日本語
![](img/lk-miru.gif)
- PDB-3ao1: Fragment-based approach to the design of ligands targeting a nove... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ao1 | ||||||
---|---|---|---|---|---|---|---|
Title | Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase | ||||||
![]() | POL polyprotein | ||||||
![]() | VIRAL PROTEIN/TRANSFERASE INHIBITOR / DNA INTEGRATION / AIDS / INTEGRASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNaseH / Fragment binding / VIRAL PROTEIN-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wielens, J. / Parker, M.W. / Chalmers, D.K. / Scanlon, M.J. | ||||||
![]() | ![]() Title: Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1 Authors: Wielens, J. / Headey, S.J. / Deadman, J.J. / Rhodes, D.I. / Parker, M.W. / Chalmers, D.K. / Scanlon, M.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3ao2C ![]() 3ao3C ![]() 3ao4C ![]() 3ao5C ![]() 3ovnC ![]() 3l3uS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17802.174 Da / Num. of mol.: 2 / Fragment: Integrase CATALYTIC CORE DOMAIN, 765-927 / Mutation: C56S, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2007 Details: double crystal monochromator and K-B pair of biomorph mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62 Å / Num. all: 24972 / Num. obs: 24930 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.093 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.52 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L3U Resolution: 1.9→49.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.818 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|