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Open data
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Basic information
Entry | Database: PDB / ID: 3vtp | ||||||
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Title | HIV fusion inhibitor MT-C34 | ||||||
![]() | (Transmembrane protein gp41![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yao, X. / Waltersperger, S. / Wang, M. / Cui, S. | ||||||
![]() | ![]() Title: The M-T hook structure is critical for design of HIV-1 fusion inhibitors. Authors: Chong, H. / Yao, X. / Sun, J. / Qiu, Z. / Zhang, M. / Waltersperger, S. / Wang, M. / Cui, S. / He, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.9 KB | Display | ![]() |
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PDB format | ![]() | 30.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 |
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Links
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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: 4899.677 Da / Num. of mol.: 1 / Fragment: N-peptide, UNP RESIDUES 555-595 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) ![]() ![]() ![]() |
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#2: Protein/peptide | ![]() Mass: 4507.922 Da / Num. of mol.: 1 / Fragment: NHR, UNP RESIDUES 631-666 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1M MES, 12 %(w/v) PEG 10000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Monochromator: Osmic VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→31.403 Å / Num. all: 6812 / Num. obs: 6812 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.64 % / Rmerge(I) obs: 0.053 / Rsym value: 0.059 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.316 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3VGX Resolution: 1.9→31.403 Å / SU ML: 0.16 / Cross valid method: RANDOM / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.888 Å2 / ksol: 0.498 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→31.403 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: 2
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