SMTL ID : 7qui.1

Crystal structure of the N-terminal domain of Siglec-8 in complex with sulfonamide sialoside analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-dimer

Ligands

2 x F9I: (2~{S},4~{S},5~{R},6~{R})-5-acetamido-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-acetamido-2-(hydroxymethyl)-4,6-bis(oxidanyl)oxan-3-yl]oxy-3,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-4-yl]oxy-6-[(1~{R},2~{R})-3-(naphthalen-2-ylsulfonylamino)-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid(Non-covalent)

F9I.1: 17 residues within 4Å: Chain A: Y.7, Y.11, R.56, P.57, Y.58, R.109, K.116, W.117, S.118, K.120, Q.122, L.123, Y.125 Chain B: S.121, Q.122, L.123 Ligands: F9I.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.122, A:Y.125, A:Y.125 Hydrogen bonds: A:Y.7, A:Y.7, A:R.56, A:Y.58, A:Y.58, A:R.109, A:K.116, A:S.118, A:K.120, A:Q.122, B:S.121 Salt bridges: A:R.109 pi-Stacking: A:Y.7 F9I.2: 13 residues within 4Å: Chain B: Y.7, Y.11, R.56, P.57, Y.58, R.109, K.116, W.117, S.118, K.120, Q.122, Y.125 Ligands: F9I.1 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.7, B:Y.7, B:W.117, B:Q.122, B:Y.125 Hydrogen bonds: B:Y.7, B:Y.7, B:R.56, B:Y.58, B:R.109, B:K.116, B:K.116, B:S.118, B:K.120, B:Q.122 Salt bridges: B:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenza, M.P. et al., Structures of the Inhibitory Receptor Siglec-8 in Complex with a High-Affinity Sialoside Analogue and a Therapeutic Antibody. Jacs Au (2023)

Release Date

2023-01-18

Peptides

Sialic acid-binding Ig-like lectin 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Sialic acid-binding Ig-like lectin 8

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