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- PDB-1v6l: Peanut lectin-lactose complex in the presence of 9mer peptide (PV... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v6l | |||||||||
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Title | Peanut lectin-lactose complex in the presence of 9mer peptide (PVIWSSATG) | |||||||||
![]() | Galactose-binding lectin | |||||||||
![]() | SUGAR BINDING PROTEIN / Lectin / open quaternary association / orthorhombic / carbohydrate specificity / protein crystallography / agglutinin | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N.C. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. | |||||||||
![]() | ![]() Title: Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. Authors: Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. #1: ![]() Title: Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. #2: ![]() Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal ...Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site Authors: Ravishankar, R. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.8 KB | Display | ![]() |
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PDB format | ![]() | 154.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v6iC ![]() 1v6jC ![]() 1v6kC ![]() 1v6mC ![]() 1v6nC ![]() 1v6oC 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24706.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | #3: Polysaccharide | |
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-Non-polymers , 3 types, 370 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: hanging drop method / pH: 4.6 Details: PEG 8000, 0.2M calcium acetate, 0.1M cacodylate pH 6.5, pH 4.6, Hanging drop method, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 43781 / Num. obs: 41998 / Redundancy: 2.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 2.5→2.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.461 / Num. unique all: 2143 |
Reflection | *PLUS % possible obs: 96.5 % / Num. measured all: 120907 |
Reflection shell | *PLUS % possible obs: 98.5 % / Num. unique obs: 2143 / Num. measured obs: 5785 |
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Processing
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Refinement | Method to determine structure: isomorphous replacement / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 134860.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6238 Å2 / ksol: 0.312193 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.224 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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