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- PDB-5cna: REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cna | |||||||||
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Title | REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE | |||||||||
![]() | CONCANAVALIN A | |||||||||
![]() | LECTIN(AGGLUTININ) | |||||||||
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. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. | |||||||||
![]() | ![]() Title: Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 A resolution and comparison with the saccharide-free structure. Authors: Naismith, J.H. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb, A.J. / Yariv, J. #1: ![]() Title: High-Resolution Structures of Single-Metal-Substituted Concanavalin A: The Co,Ca-Protein at 1.6 Angstroms and the Ni,Ca-Protein at 2.0 Angstroms Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. #2: ![]() Title: Refined Structure of Cadmium-Substituted Concanavalin a at 2.0 Angstroms Resolution Authors: Naismith, J.H. / Habash, J. / Harrop, S. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J. #3: ![]() Title: High-Resolution Crystallographic Studies of Native Concanavalin a Using Rapid Laue Data Collection Methods and the Introduction of a Monochromatic Large-Angle Oscillation Technique (Lot) Authors: Weisgerber, S. / Helliwell, J.R. #4: ![]() Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage Authors: Min, W. / Dunn, A.J. / Jones #5: ![]() Title: The Structure of the Saccharide Binding-Site of Concanavalin A Authors: Derewenda, Z. / Yariv, J. / Helliwell, J.R. / Kalb(Gilboa), A.J. / Dodson, E.J. / Papiz, M.Z. / Wan, T. / Campbell, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.3 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.1 KB | Display | ![]() |
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Full document | ![]() | 488 KB | Display | |
Data in XML | ![]() | 43.2 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Atom site foot note | 1: ALA A 207 - ASP A 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA B 207 - ASP B 208 OMEGA =359.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA C 207 - ASP C 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ALA D 207 - ASP D 208 OMEGA = 1.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: THE ATOMS LABELLED OD1 AND OD2 IN ASP 10 OF EACH SUBUNIT HAVE BEEN INTERCHANGED COMPARED WITH THE LABELS IN THE PUBLISHED PAPERS. |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/MMA.gif)
![](data/chem/img/MMA.gif)
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-MMA / |
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-Non-polymers , 4 types, 542 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, LISTED AS REFERENCE 3 ABOVE. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 58871 / % possible obs: 82 % / Observed criterion σ(F): 1 / Num. measured all: 62198 / Rmerge(I) obs: 0.076 |
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Processing
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Refinement | Resolution: 2→8 Å / σ(F): 1 Details: THE THREE RAMACHANDRAN OUTLIERS THR A 120, HIS A 121 AND SER B 204) DESCRIBED IN NAISMITH ET AL. ARE IN POORLY DEFINED REGIONS OF ELECTRON DENSITY.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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