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- PDB-4r6o: Jacalin-carbohydrate interactions. Distortion of the ligand as a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r6o | ||||||
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Title | Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity. | ||||||
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![]() | SUGAR BINDING PROTEIN / Galactose specific lectin / beta-prism I fold / post translational proteolysis / T-antigen binding protein / Plant lectins / Galactose | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity. Authors: Abhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M. #1: ![]() Title: A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold. Authors: Sankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M. #2: ![]() Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes. Authors: Jeyaprakash, A.A. / Geetha Rani, P. / Banuprakash Reddy, G. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M. #3: ![]() Title: Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study. Authors: Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. #4: ![]() Title: Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity. Authors: Arockia Jeyaprakash, A. / Jayashree, G. / Mahanta, S.K. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. #5: ![]() Title: Structural basis for the unusual carbohydrate-binding specificity of jacalin towards galactose and mannose. Authors: Bourne, Y. / Astoul, C.H. / Zamboni, V. / Peumans, W.J. / Menu-Bouaouiche, L. / Van Damme, E.J. / Barre, A. / Rouge, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 528.6 KB | Display | ![]() |
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Full document | ![]() | 537 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r6nC ![]() 4r6pC ![]() 4r6qC ![]() 4r6rC ![]() 1ku8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide / Sugars , 3 types, 12 molecules ACEGBDFH![](data/chem/img/GLA.gif)
![](data/chem/img/GLA.gif)
#1: Protein | Mass: 14673.479 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-20 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 1944.170 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Sugar | ChemComp-GLA / |
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-Non-polymers , 4 types, 690 molecules ![](data/chem/img/ZZ1.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZZ1 / #5: Chemical | ChemComp-IPA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% PEG 8000, 0.1M HEPES, pH 7.4, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2013 / Details: Bent collimating mirror and toroid | ||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→60.62 Å / Num. all: 83181 / Num. obs: 83181 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.089 / Net I/σ(I): 8.2 | ||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KU8 Resolution: 1.6→28.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.034 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.066 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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