5TG3
Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man
Summary for 5TG3
| Entry DOI | 10.2210/pdb5tg3/pdb |
| Descriptor | Dioclea reflexa lectin, CALCIUM ION, MANGANESE (II) ION, ... (5 entities in total) |
| Functional Keywords | lectin, dioclea reflexa, drfl, x-man, sugar binding protein |
| Biological source | Dioclea reflexa |
| Total number of polymer chains | 4 |
| Total formula weight | 104359.74 |
| Authors | Santiago, M.Q.,Correia, J.L.A.,Pinto-Junior, V.R.,Osterne, V.J.S.,Pereira, R.I.,Silva-Filho, J.C.,Lossio, C.F.,Rocha, B.A.M.,Delatorre, P.,Neco, A.H.B.,Araripe, D.A.,Nascimento, K.S.,Cavada, B.S. (deposition date: 2016-09-27, release date: 2017-02-15, Last modification date: 2023-10-04) |
| Primary citation | Pinto-Junior, V.R.,Osterne, V.J.,Santiago, M.Q.,Correia, J.L.,Pereira-Junior, F.N.,Leal, R.B.,Pereira, M.G.,Chicas, L.S.,Nagano, C.S.,Rocha, B.A.,Silva-Filho, J.C.,Ferreira, W.P.,Rocha, C.R.,Nascimento, K.S.,Assreuy, A.M.,Cavada, B.S. Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics. Int. J. Biol. Macromol., 98:12-23, 2017 Cited by PubMed Abstract: The three-dimensional structure of Dioclea reflexa seed lectin (DrfL) was studied in detail by a combination of X-ray crystallography, molecular docking and molecular dynamics. DrfL was purified by affinity chromatography using Sephadex G-50 matrix. Its primary structure was obtained by mass spectrometry, and crystals belonging to orthorhombic space group P222 were grown by the vapor diffusion method at 293K. The crystal structure was solved at 1.765Å and was very similar to that of other lectins from the same subtribe. The structure presented R and R of 21.69% and 24.89%, respectively, with no residues in nonallowed regions of Ramachandran plot. Similar to other Diocleinae lectins, DrfL was capable of relaxing aortic rings via NO induction, with CRD participation, albeit with low intensity (32%). In silico analysis results demonstrated that DrfL could strongly interact with complex N-glycans, components of blood vessel glycoconjugates. Despite the high similarity among Diocleinae lectins, it was also reported that each lectin has unique CRD properties that influence carbohydrate binding, resulting in different biological effects presented by these molecules. PubMed: 28130130DOI: 10.1016/j.ijbiomac.2017.01.092 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.765 Å) |
Structure validation
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