+Open data
-Basic information
Entry | Database: PDB / ID: 3w19 | ||||||
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Title | Potent HIV fusion inhibitor CP32M-2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/INHIBITOR / 6-helix-bundle / MT-hook / inhibit HIV membrane fusion / MEMBRANE PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm ...host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.278 Å | ||||||
Authors | Yao, X. / Waltersperger, S. / Wang, M.T. / Cui, S. | ||||||
Citation | Journal: To be Published Title: Optimization of novel anti-HIV fusion inhibitor Authors: Yao, X. / Waltersperger, S. / Wang, M.T. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w19.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w19.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w19 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w19 | HTTPS FTP |
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-Related structure data
Related structure data | 3vgxS 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4515.291 Da / Num. of mol.: 1 / Fragment: N-peptide T21, UNP RESIDIES 552-589 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HIV-1 VIRUS / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375 |
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#2: Protein/peptide | Mass: 3825.257 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THIS SEQUENCE DOES NOT OCCUR NATURALLY IN HIV-1, BUT DESIGNED BASED ON SEQUENCE OF HIV-1 GP41 CHR AND ITS PARENTAL PEPTIDE CP32M |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Ammonium sulfate, 0.1 M HEPES, 16%(w/v) PEG 4000, 10%(w/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.82656 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011 |
Radiation | Monochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 1.278→36.144 Å / Num. all: 21170 / Num. obs: 21170 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 27.92 |
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.49 / Num. unique all: 3334 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3VGX Resolution: 1.278→36.14 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 14.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.505 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.278→36.14 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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