[English] 日本語
![](img/lk-miru.gif)
- PDB-1a5v: ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND M... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1a5v | ||||||
---|---|---|---|---|---|---|---|
Title | ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION | ||||||
![]() | INTEGRASE | ||||||
![]() | HYDROLASE / ENDONUCLEASE / HIV-1 INTEGRASE INHIBITOR | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A. | ||||||
![]() | ![]() Title: Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor. Authors: Lubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A. / Zhao, H. / Burke Jr., T.R. / Neamati, N. / Pommier, Y. / Merkel, G. / Skalka, A.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 46.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1a5wC ![]() 1a5xC ![]() 1asvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | THE AUTHOR MAINTAINS THAT THE BIOLOGICAL UNIT IS NOT YET KNOWN. THE MINIMUM MULTIMER IS BELIEVED TO CONTAIN AT LEAST THE DIMER GENERATED BT THE TRANSFORMATION IN REMARK 350, SHOWN IN BOTH HIV-1 AND ASV INTEGRASE CORE DOMAIN STRUCTURES. |
-
Components
#1: Protein | Mass: 17398.922 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN Source method: isolated from a genetically manipulated source Details: P03354 FRAGMENT OF POLYPROTEIN POL-RSVP Source: (gene. exp.) ![]() Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / Description: SEE JRNL REFERENCE / Plasmid: PRC23IN(52-207) / Production host: ![]() ![]() References: UniProt: P03354, UniProt: O92956*PLUS, RNA-directed DNA polymerase |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-Y3 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...THE APPARENT DISCREPANC |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 38 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1M NA HEPES, PH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Aug 5, 1997 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 14653 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.16 % / Rsym value: 0.066 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.354 / % possible all: 98.1 |
Reflection | *PLUS Num. measured all: 92081 / Rmerge(I) obs: 0.066 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ASV Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2 Details: ATOMIC OCCUPANCIES OF DISORDERED ATOMS ARE SET TO 0.00 IN THE COORDINATES,
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|