SMTL ID : 5u3e.1

Crystal Structure of Native Lectin from Canavalia bonariensis Seeds (CaBo) complexed with alpha-methyl-D-mannoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.1: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:L.99, A:Y.100, A:Y.100, A:N.168, A:R.228 MMA.4: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.14, B:L.99, B:Y.100, B:Y.100, B:N.168, B:R.228 MMA.7: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:L.99, C:Y.100, C:Y.100, C:N.168, C:R.228 Water bridges: C:Y.12 MMA.10: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:L.99, D:Y.100, D:Y.100, D:N.168, D:R.228 Water bridges: D:Y.12

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1, H2O.2 MN.5: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.6, H2O.7 MN.8: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.10, H2O.11 MN.11: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.15, H2O.16

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19, H2O.6 CA.9: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19, H2O.10 CA.12: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.15

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Cavada, B.S. et al., Canavalia bonariensis lectin: Molecular bases of glycoconjugates interaction and antiglioma potential. Int. J. Biol. Macromol. (2018)

Release Date

2017-08-23

Peptides

Canavalia bonariensis seed lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Canavalia bonariensis seed lectin