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Yorodumi- PDB-5tyr: X-ray crystal structure of wild type HIV-1 protease in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tyr | |||||||||
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Title | X-ray crystal structure of wild type HIV-1 protease in complex with GRL-121 | |||||||||
Components | Protease | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / GRL-121 / HIV-1 PROTEASE / PROTEASE-INHIBITOR / DARUNAVIR / PYRAN / FURAN / NONPEPTIDIC / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / AIDS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Yedidi, R.S. / Hayashi, H. / Aoki, M. / Das, D. / Ghosh, A.K. / Mitsuya, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2017 Title: A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency. Authors: Aoki, M. / Hayashi, H. / Rao, K.V. / Das, D. / Higashi-Kuwata, N. / Bulut, H. / Aoki-Ogata, H. / Takamatsu, Y. / Yedidi, R.S. / Davis, D.A. / Hattori, S.I. / Nishida, N. / Hasegawa, K. / ...Authors: Aoki, M. / Hayashi, H. / Rao, K.V. / Das, D. / Higashi-Kuwata, N. / Bulut, H. / Aoki-Ogata, H. / Takamatsu, Y. / Yedidi, R.S. / Davis, D.A. / Hattori, S.I. / Nishida, N. / Hasegawa, K. / Takamune, N. / Nyalapatla, P.R. / Osswald, H.L. / Jono, H. / Saito, H. / Yarchoan, R. / Misumi, S. / Ghosh, A.K. / Mitsuya, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tyr.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tyr.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/5tyr ftp://data.pdbj.org/pub/pdb/validation_reports/ty/5tyr | HTTPS FTP |
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-Related structure data
Related structure data | 5tysC 4hlaS 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: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: C8B467, UniProt: G0X8E8*PLUS #2: Chemical | ChemComp-7O7 / ( | #3: 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: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M 2-morpholinoethanesulfonic acid (pH 6.5), 25% (w/v) polyethylene glycol 4000, 0.2 M potassium iodide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 20171 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.05 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.55 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HLA Resolution: 1.8→45.317 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 24.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.317 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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