1NXD

Crystal structure of MnMn Concanavalin A

Summary for 1NXD

• Entry DOI: 10.2210/pdb1nxd/pdb
• Descriptor: concanavalin A, AZIDE ION, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: lectin, metal binding protein
• Biological source: Canavalia ensiformis (jack bean); More
• Total number of polymer chains: 4
• Total formula weight: 105995.67

Authors

Lopez-Jaramillo, F.J.,Gonzalez-Ramirez, L.A.,Albert, A.,Santoyo-Gonzalez, F.,Vargas-Berenguel, A.,Otalora, F. (deposition date: 2003-02-10, release date: 2004-03-30, Last modification date: 2023-08-16)

Primary citation

Lopez-Jaramillo, F.J.,Gonzalez-Ramirez, L.A.,Albert, A.,Santoyo-Gonzalez, F.,Vargas-Berenguel, A.,Otalora, F.
Structure of concanavalin A at pH 8: bound solvent and crystal contacts.
Acta Crystallogr.,Sect.D, 60:1048-1056, 2004

PubMed Abstract: Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.

PubMed: 15159564
DOI: 10.1107/S0907444904007000

Experimental method

X-RAY DIFFRACTION (1.9 Å)