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- PDB-3d4k: Concanavalin A Complexed to a Synthetic Analog of the Trimannoside -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d4k | |||||||||
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Title | Concanavalin A Complexed to a Synthetic Analog of the Trimannoside | |||||||||
![]() | Concanavalin-A | |||||||||
![]() | SUGAR BINDING PROTEIN / Concanavalin A / Conserved Water / Carbohydrate-Protein Binding / Glycoprotein / Lectin / Manganese / Metal-binding | |||||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Kadirvelraj, R. / Foley, B.L. / Dyekjaer, J.D. / Woods, R.J. | |||||||||
![]() | ![]() Title: Involvement of water in carbohydrate-protein binding: concanavalin A revisited. Authors: Kadirvelraj, R. / Foley, B.L. / Dyekjaer, J.D. / Woods, R.J. #1: Journal: J.Am.Chem.Soc. / Year: 2001 Title: Involvement of water in carbohydrate-protein binding. Authors: Clarke, C. / Woods, R.J. / Gluska, J. / Cooper, A. / Nutley, M.A. / Boons, G.J. #2: ![]() 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 | ![]() | 208.7 KB | Display | ![]() |
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PDB format | ![]() | 165.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qd0S 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Jack-bean / Source: (natural) ![]() ![]() #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside Type: oligosaccharide / Mass: 546.518 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 584 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 10-16% PEG 6000, 100 mM Sodium cacodylate, 50 mM NaCL, 1 mM MnCL2, 1 mM CaCL2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2002 / Details: Mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 88130 / Num. obs: 87296 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.036 / Χ2: 1.057 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.01 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8649 / Rsym value: 0.502 / Χ2: 1.063 / % possible all: 98.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.576 / Cor.coef. Fo:Fc: 0.13 / Cor.coef. Io to Ic: 0.12
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1QD0 Resolution: 1.8→30 Å / FOM work R set: 0.83 / Isotropic thermal model: Isotropic / Cross valid method: SigmaA / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.702 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.552 Å2
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Refine analyze | Luzzati coordinate error obs: 0.223 Å / Luzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.076 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Xplor file |
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