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- PDB-4chz: Interrogating HIV integrase for compounds that bind- a SAMPL challenge -
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Open data
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Basic information
Entry | Database: PDB / ID: 4chz | ||||||
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Title | Interrogating HIV integrase for compounds that bind- a SAMPL challenge | ||||||
![]() | INTEGRASE | ||||||
![]() | TRANSFERASE / STRUCTURE BASED DRUG DESIGN | ||||||
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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793.6 KB | Display | ![]() |
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Full document | ![]() | 796.8 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() 4cieC ![]() 4cifC ![]() 4cigC ![]() 4cj3C ![]() 4cj4C ![]() 4cj5C ![]() 4cjeC ![]() 4cjfC ![]() 4cjkC ![]() 4cjlC ![]() 4cjpC ![]() 4cjqC ![]() 4cjrC ![]() 4cjsC ![]() 4cjtC ![]() 4cjuC ![]() 4cjvC ![]() 4cjwC ![]() 4ck1C ![]() 4ck2C ![]() 4ck3C ![]() 4ovlC ![]() 3zsqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20044.672 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 50-212 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76353, UniProt: P12497*PLUS, DNA-directed DNA polymerase |
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-Non-polymers , 7 types, 178 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/H75.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/H75.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-H75 / | #7: Chemical | ChemComp-LYS / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→66.8 Å / Num. obs: 37971 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZSQ Resolution: 1.8→45.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.982 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ALTHOUGH THERE IS A DIMER IN THE ASYMMETRIC UNIT, ONLY ONE OF TWO POSSIBLE COMPOUNDS WAS PUT INTO DENSITY, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ALTHOUGH THERE IS A DIMER IN THE ASYMMETRIC UNIT, ONLY ONE OF TWO POSSIBLE COMPOUNDS WAS PUT INTO DENSITY, AS IT DOESN'T FIT THE DENSITY THAT WELL. SO THERE IS 'EXTRA' UNMODELLED DENSITY FOR ONE COMPOUND.
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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: 27.958 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.33 Å
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Refine LS restraints |
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