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- PDB-3kfn: HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kfn | ||||||
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Title | HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 / PROTEASE / EXO SITE / Aspartyl protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Stout, C.D. | ||||||
![]() | ![]() Title: Fragment-based screen against HIV protease. Authors: Perryman, A.L. / Zhang, Q. / Soutter, H.H. / Rosenfeld, R. / McRee, D.E. / Olson, A.J. / Elder, J.E. / David Stout, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kf0C ![]() 3kfpC ![]() 3kfrC ![]() 3kfsC ![]() 4e43C ![]() 2az8S S: Starting model for refinement C: citing same article ( |
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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: 10831.833 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q903N5, UniProt: P12499*PLUS, HIV-1 retropepsin |
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-Non-polymers , 6 types, 210 molecules ![](data/chem/img/3TL.gif)
![](data/chem/img/4DX.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4DX.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-3TL / | ||||||
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#3: Chemical | ChemComp-4DX / ( | ||||||
#4: Chemical | ChemComp-DMS / #5: Chemical | #6: Chemical | ChemComp-BME / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 0.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2009 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→48.564 Å / Num. all: 23368 / Num. obs: 21896 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 3 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1574 / Rsym value: 0.637 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HIV PR dimer generated from PDB entry 2AZ8 Resolution: 1.77→48.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.905 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.153 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.23 Å2 / Biso mean: 32.903 Å2 / Biso min: 18.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→48.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Total num. of bins used: 20
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