SMTL ID : 6z6y.1

Galectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

1 x L4L: [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2-acetamido-3-oxidanylidene-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate(Non-covalent)

L4L.1: 12 residues within 4Å: Chain A: R.41, Q.43, R.55, H.61, N.63, R.65, V.73, N.75, W.82, E.85 Ligands: ACT.5, PGE.8 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:Q.43, A:H.61, A:N.63, A:R.65, A:N.75, A:W.82 Water bridges: A:R.65 Salt bridges: A:R.41, A:R.55, A:H.61, A:R.65

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: I.126, G.127, E.129, K.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.127 Salt bridges: A:K.130 ACT.3: 4 residues within 4Å: Chain A: I.87, T.88, Y.89, D.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.89, A:D.90 ACT.4: 5 residues within 4Å: Chain A: V.16, G.17, T.18, S.50, T.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.50 Water bridges: A:V.16, A:T.18 ACT.5: 6 residues within 4Å: Chain A: R.55, L.77, E.80, K.81, W.82 Ligands: L4L.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.82 Salt bridges: A:R.55 ACT.6: 6 residues within 4Å: Chain A: Q.22, L.23, D.24, P.25, P.128, E.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.22, A:D.24 ACT.7: 6 residues within 4Å: Chain A: P.54, R.55, A.56, D.57, N.79, E.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.55, A:N.79 Water bridges: A:E.80

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 8 residues within 4Å: Chain A: R.41, Q.43, S.51, M.52, R.55, Y.137, G.138 Ligands: L4L.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.41, A:R.55 Water bridges: A:R.41, A:R.41, A:Y.137, A:K.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, P.V. et al., Probing sulfatide-tissue lectin recognition with functionalized glycodendrimersomes. Iscience (2021)

Release Date

2020-12-30

Peptides

Galectin-8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Galectin-8