SMTL ID : 5uuy.1

Crystal structure of Dioclea lasiocarpa lectin (DLL) complexed with X-MAN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 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.2 MN.4: 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.8, H2O.8 MN.7: 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.13, H2O.13 MN.10: 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.19, H2O.19

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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:Y.12, A:D.19, H2O.3, H2O.3 CA.5: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.8, H2O.9 CA.8: 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.14, H2O.14 CA.11: 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.19, H2O.19

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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.99 Hydrogen bonds: A:N.14, A:L.99, A:Y.100, A:Y.100, A:Y.100, A:Y.100, A:R.228 Water bridges: A:G.226 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.99 Hydrogen bonds: B:N.14, B:L.99, B:Y.100, B:Y.100, B:Y.100, B:Y.100, B:R.228 Water bridges: B:G.226 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 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.99 Hydrogen bonds: C:N.14, C:L.99, C:Y.100, C:Y.100, C:Y.100, C:R.228 Water bridges: C:G.226 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:L.99, D:Y.100, D:Y.100, D:Y.100, D:R.228 Water bridges: D:G.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nascimento, K.S. et al., Structural analysis of Dioclea lasiocarpa lectin: A C6 cells apoptosis-inducing protein. Int. J. Biochem. Cell Biol. (2017)

Release Date

2017-10-04

Peptides

Dioclea lasiocarpa lectin (DLL): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dioclea lasiocarpa lectin (DLL)