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Yorodumi- PDB-4i54: Crystal structure of clade A/E 93TH057 HIV-1 gp120 H375S core in ... -
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-Basic information
Entry | Database: PDB / ID: 4i54 | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 H375S core in complex with DMJ-II-121 | ||||||
Components | HIV-1 glycoprotein | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV / gp120 / entry inhibitor / structure-based drug design / thermodynamics / viral inhibition / DMJ-II-121 / CD4-mimetic / VIRAL PROTEIN-INHIBITOR COMPLEX / Clade A/E / CD4 / Extracellular | ||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Le-Khac, M. / Hendrickson, W.A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2013 Title: Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. Authors: Lalonde, J.M. / Le-Khac, M. / Jones, D.M. / Courter, J.R. / Park, J. / Schon, A. / Princiotto, A.M. / Wu, X. / Mascola, J.R. / Freire, E. / Sodroski, J. / Madani, N. / Hendrickson, W.A. / Smith, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i54.cif.gz | 288.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i54.ent.gz | 246.1 KB | Display | PDB format |
PDBx/mmJSON format | 4i54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/4i54 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i54 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: A/E 93TH057 / Plasmid: PVRC8400 / Cell line (production host): 293F / Production host: Homo Sapiens (human) / References: UniProt: Q0ED31*PLUS #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-NAG / #5: 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: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 8000, 5% ISO-PROPANOL, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2012 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.205→94.432 Å / Num. obs: 40186 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33.628 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33.628 Å
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Refine LS restraints |
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LS refinement shell |
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