[English] 日本語
Yorodumi- PDB-4ovl: Interrogating HIV integrase for compounds that bind- a SAMPL challenge -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ovl | ||||||
---|---|---|---|---|---|---|---|
Title | Interrogating HIV integrase for compounds that bind- a SAMPL challenge | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE / HIV INTEGRASE / STRUCTURE BASED DRUG DESIGN | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / endonuclease activity / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Peat, T.S. | ||||||
Citation | Journal: J. Comput. Aided Mol. Des. / Year: 2014 Title: Interrogating HIV integrase for compounds that bind--a SAMPL challenge. Authors: Peat, T.S. / Dolezal, O. / Newman, J. / Mobley, D. / Deadman, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ovl.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ovl.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ovl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/4ovl ftp://data.pdbj.org/pub/pdb/validation_reports/ov/4ovl | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ce9C 4ceaC 4cebC 4cecC 4cedC 4ceeC 4cefC 4ceoC 4ceqC 4cerC 4cesC 4cezC 4cf0C 4cf1C 4cf2C 4cf8C 4cf9C 4cfaC 4cfbC 4cfcC 4cfdC 4cgdC 4cgfC 4cggC 4cghC 4cgiC 4cgjC 4chnC 4choC 4chpC 4chqC 4chyC 4chzC 4cieC 4cifC 4cigC 4cj3C 4cj4C 4cj5C 4cjeC 4cjfC 4cjkC 4cjlC 4cjpC 4cjqC 4cjrC 4cjsC 4cjtC 4cjuC 4cjvC 4cjwC 4ck1C 4ck2C 4ck3C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 57 - 209 / Label seq-ID: 28 - 180
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20044.672 Da / Num. of mol.: 2 / Mutation: C56S, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: PET / Production host: Escherichia coli (E. coli) References: UniProt: Q76353, UniProt: P12497*PLUS, nicotinamide-nucleotide adenylyltransferase |
---|
-Non-polymers , 6 types, 154 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACY / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 mM TRIS PH 8.0, 250 mM NACL, 30 mM MGCL2, 5 mM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 mM SODIUM ACETATE BUFFER PH 5.0 TO 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95661 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95661 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.6 Å / Num. obs: 42336 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2 / Num. measured obs: 6138 |
-Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.949 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.766 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→45.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|