+Open data
-Basic information
Entry | Database: PDB / ID: 5zpw | ||||||
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Title | Generation of a long-acting fusion inhibitor against HIV-1 | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Inhibitor / Complex / VIRUS | ||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / viral process / host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å | ||||||
Authors | Guo, Y. / Shi, X.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Medchemcomm / Year: 2018 Title: Generation of a long-acting fusion inhibitor against HIV-1. Authors: Guo, Y. / Zhou, P.P. / Zhang, S.Y. / Fan, X.W. / Dou, Y.W. / Shi, X.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zpw.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zpw.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/5zpw ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zpw | HTTPS FTP |
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-Related structure data
Related structure data | 3vu6S S: Starting model for refinement |
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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/peptide | Mass: 4133.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: D6NUQ7, UniProt: A0A1S6KGE5*PLUS #2: Protein/peptide | Mass: 3083.719 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: PEG 400, magnesium chloride, 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.199→21.184 Å / Num. obs: 11745 / % possible obs: 98.14 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.58 |
Reflection shell | Resolution: 2.199→2.278 Å / Rmerge(I) obs: 0.611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VU6 Resolution: 2.199→19.626 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 31.11 / 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: 2.199→19.626 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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