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Open data
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Basic information
Entry | Database: PDB / ID: 1jyi | ||||||
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Title | CONCANAVALIN A/12-MER PEPTIDE COMPLEX | ||||||
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![]() | SUGAR BINDING PROTEIN / LECTIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() | ||||||
![]() | Jain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.M. | ||||||
![]() | ![]() Title: Structural and Functional Consequences of Peptide-carbohydrate Mimicry. Crystal Structure of a Carbohydrate-mimicking Peptide Bound to Concanavalin A. Authors: Jain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.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 | ![]() | 189.8 KB | Display | ![]() |
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PDB format | ![]() | 154.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cnaS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 1365.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.32 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 9 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→10 Å / Num. obs: 34767 / % possible obs: 86.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.67 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.75→10 Å |
Reflection | *PLUS Redundancy: 3 % / Num. measured all: 47255 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Lowest resolution: 3.07 Å / % possible obs: 67.5 % |
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Processing
Software |
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Refinement | Starting model: 5CNA Resolution: 2.75→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.192 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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