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Yorodumi- PDB-5cmz: Artificial HIV fusion inhibitor AP3 fused to the C-terminus of gp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cmz | ||||||
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Title | Artificial HIV fusion inhibitor AP3 fused to the C-terminus of gp41 NHR | ||||||
Components |
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Keywords | VIRAL PROTEIN/INHIBITOR / Enfuvirtide / HIV fusion inhibitor / AP3 / gp41 / 6-HB / 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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.574 Å | ||||||
Authors | Zhu, Y. / Ye, S. / Zhang, R. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy. Authors: Zhu, X. / Zhu, Y. / Ye, S. / Wang, Q. / Xu, W. / Su, S. / Sun, Z. / Yu, F. / Liu, Q. / Wang, C. / Zhang, T. / Zhang, Z. / Zhang, X. / Xu, J. / Du, L. / Liu, K. / Lu, L. / Zhang, R. / Jiang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cmz.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cmz.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/5cmz ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cmz | 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 on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 5230.056 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q1HMR5, UniProt: P04578*PLUS #2: Protein/peptide | Mass: 4682.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 40 molecules
#3: Chemical | ChemComp-SO4 / |
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#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-P4G / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03317 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→38 Å / Num. obs: 61523 / % possible obs: 99.9 % / Redundancy: 7.7 % / Net I/σ(I): 27.2 |
-Processing
Software |
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Refinement | Resolution: 2.574→37.983 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.98 / 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: 2.574→37.983 Å
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Refine LS restraints |
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LS refinement shell |
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