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- PDB-1tei: STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tei | |||||||||
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Title | STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA-D-MAN-(1,6)[BETA-D-GLCNAC(1,2)ALPHA-D-MAN (1,6)]ALPHA-D-MAN | |||||||||
![]() | CONCANAVALIN A | |||||||||
![]() | LECTIN / CONCANAVALIN A / PENTASACCHARIDE BINDING / RECOGNITION COMPLEX | |||||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Naismith, J.H. / Moothoo, D.N. | |||||||||
![]() | ![]() Title: Concanavalin A distorts the beta-GlcNAc-(1-->2)-Man linkage of beta-GlcNAc-(1-->2)-alpha-Man-(1-->3)-[beta-GlcNAc-(1-->2)-alpha-Man- (1-->6)]-Man upon binding. Authors: Moothoo, D.N. / Naismith, J.H. #1: ![]() Title: Structural Basis of Trimannoside Recognition by Concanavalin A Authors: Naismith, J.H. / Field, R.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 | ![]() | 375.8 KB | Display | ![]() |
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PDB format | ![]() | 311.1 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source #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: 2.36 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: POLYETHYLENE GLYCOL 15%, pH 5.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Oct 29, 1996 / Details: MIRRORS, MACSCIENCE |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 53516 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.337 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5CNA Resolution: 2.7→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: X-PLOR / σ(F): 0 Details: ATOMS WITH ZERO OCCUPANCY (443 OUT OF 14472 PROTEIN ATOMS, 25 OUT OF 496 SUGAR ATOMS) ARE STEREOCHEMICALLY MODELED. THE LOOP AT RESIDUE 120 IS KNOWN TO BE PARTIALLY CLEAVED IN THE PROTEIN ...Details: ATOMS WITH ZERO OCCUPANCY (443 OUT OF 14472 PROTEIN ATOMS, 25 OUT OF 496 SUGAR ATOMS) ARE STEREOCHEMICALLY MODELED. THE LOOP AT RESIDUE 120 IS KNOWN TO BE PARTIALLY CLEAVED IN THE PROTEIN AND WAS NOT LOCATED IN INTERPRETABLE DENSITY.
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Displacement parameters | Biso mean: 23.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Weight Biso : 3 / Weight position: 60 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2498 |