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- PDB-4ck1: 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: 4ck1 | ||||||
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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 / virion membrane / structural molecule activity / 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 | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20.1 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 ![]() 4chzC ![]() 4cieC ![]() 4cifC ![]() 4cigC ![]() 4cj3C ![]() 4cj4C ![]() 4cj5C ![]() 4cjeC ![]() 4cjfC ![]() 4cjkC ![]() 4cjlC ![]() 4cjpC ![]() 4cjqC ![]() 4cjrC ![]() 4cjsC ![]() 4cjtC ![]() 4cjuC ![]() 4cjvC ![]() 4cjwC ![]() 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 , 6 types, 143 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OM1.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OM1.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: 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: May 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→66.7 Å / Num. obs: 37523 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZSQ Resolution: 1.75→45.04 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.775 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 23.247 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.04 Å
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Refine LS restraints |
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