+Open data
-Basic information
Entry | Database: PDB / ID: 5yc0 | ||||||
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Title | Crystal structure of LP-46/N44 | ||||||
Components |
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Keywords | VIRAL PROTEIN/INHIBITOR / 6-HB / HIV-1 / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhang, X. / Wang, X. / He, Y. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Exceptional potency and structural basis of a T1249-derived lipopeptide fusion inhibitor against HIV-1, HIV-2, and simian immunodeficiency virus Authors: Zhu, Y. / Zhang, X. / Ding, X. / Chong, H. / Cui, S. / He, J. / Wang, X. / He, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yc0.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yc0.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 5yc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5yc0 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5yc0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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/peptide | Mass: 5037.884 Da / Num. of mol.: 6 / Fragment: UNP residues 27-70 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HMR5, UniProt: P04578*PLUS #2: Protein/peptide | Mass: 3893.309 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 #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: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 8%(v/v) Tacsimate pH 4.0, 20%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.1 Å / Num. obs: 26727 / % possible obs: 96 % / Redundancy: 2 % / Net I/σ(I): 12.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.098 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 28.98 / 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→27.098 Å
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Refine LS restraints |
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LS refinement shell |
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