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Open data
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Basic information
Entry | Database: PDB / ID: 7ria | ||||||
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Title | Griffithsin variant Y28A/Y68A/Y110A | ||||||
![]() | Griffithsin | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / mannose binding protein / HIV inhibitor / C3 pseudosymmetry / carbohydrate binding sites | ||||||
Function / homology | ![]() N-acetylgalactosamine binding / D-glucose binding / D-mannose binding / carbohydrate binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhao, G. / Sun, J. / Bewley, C.A. | ||||||
![]() | ![]() Title: C 3 -Symmetric Aromatic Core of Griffithsin Is Essential for Potent Anti-HIV Activity. Authors: Sun, J. / Zhao, G. / Bylund, T. / Lee, M. / Adibhatla, S. / Kwong, P.D. / Chuang, G.Y. / Rawi, R. / Bewley, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ribC ![]() 7ricC ![]() 7ridC ![]() 7rkgC ![]() 7rkiC ![]() 2gucS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14541.808 Da / Num. of mol.: 2 / Mutation: Y28A, Y68A, Y110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Q66D336 / Production host: ![]() ![]() #2: Sugar | ChemComp-MAN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M bis-tris buffer, pH 5.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.27 Å / Num. obs: 20321 / % possible obs: 99.2 % / Redundancy: 6 % / Biso Wilson estimate: 22.45 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 905 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GUC Resolution: 1.8→27.27 Å / SU ML: 0.2148 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4995 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.27 Å
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Refine LS restraints |
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LS refinement shell |
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