SMTL ID : 5tg3.1

Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:D.19, H2O.1, H2O.2 CA.4: 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.10 CA.7: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.18, H2O.20 CA.10: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.23, H2O.24

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.2, H2O.3 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.10, H2O.11 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.18, H2O.19 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.23, H2O.24

4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)

XMM.3: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:Y.12, A:N.14, A:L.99, A:Y.100, A:Y.100, A:R.228 Water bridges: A:R.228 XMM.6: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.12, B:N.14, B:L.99, B:Y.100, B:Y.100, B:R.228 Water bridges: B:N.168, B:R.228 XMM.9: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.14, C:L.99, C:Y.100, C:Y.100, C:Y.100, C:R.228 Water bridges: C:N.168, C:G.226, C:R.228 XMM.12: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.99 Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228 Water bridges: D:N.168

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Pinto-Junior, V.R. et al., Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics. Int. J. Biol. Macromol. (2017)

Release Date

2017-02-15

Peptides

Dioclea reflexa lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dioclea reflexa lectin