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Yorodumi- PDB-6b36: Crystal Structure of HIV Protease complexed with (S)-N-(3-fluoro-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b36 | ||||||
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Title | Crystal Structure of HIV Protease complexed with (S)-N-(3-fluoro-2-(2-(1-(phenylsulfonyl)piperazin-2-yl)ethyl)phenyl)-3,3-bis(4-fluorophenyl)propanamide | ||||||
Components | HIV-1 Protease | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV / protease / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.63 Å | ||||||
Authors | Su, H.P. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors. Authors: Bungard, C.J. / Williams, P.D. / Schulz, J. / Wiscount, C.M. / Holloway, M.K. / Loughran, H.M. / Manikowski, J.J. / Su, H.P. / Bennett, D.J. / Chang, L. / Chu, X.J. / Crespo, A. / Dwyer, M.P. ...Authors: Bungard, C.J. / Williams, P.D. / Schulz, J. / Wiscount, C.M. / Holloway, M.K. / Loughran, H.M. / Manikowski, J.J. / Su, H.P. / Bennett, D.J. / Chang, L. / Chu, X.J. / Crespo, A. / Dwyer, M.P. / Keertikar, K. / Morriello, G.J. / Stamford, A.W. / Waddell, S.T. / Zhong, B. / Hu, B. / Ji, T. / Diamond, T.L. / Bahnck-Teets, C. / Carroll, S.S. / Fay, J.F. / Min, X. / Morris, W. / Ballard, J.E. / Miller, M.D. / McCauley, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b36.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b36.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6b36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/6b36 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b36 | HTTPS FTP |
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-Related structure data
Related structure data | 6b38C 6b3cC 6b3fC 6b3gC 6b3hC 5ivtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10804.808 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Human immunodeficiency virus 1 / References: UniProt: P04587, HIV-1 retropepsin #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CKD / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium acetate, pH 5.0-5.5 300-500mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.631→19.31 Å / Num. obs: 153989 / % possible obs: 89.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 24.25 Å2 / Net I/σ(I): 19.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ivt Resolution: 1.63→19.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.087
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Displacement parameters | Biso mean: 26.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.63→19.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.7 Å / Total num. of bins used: 13
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