SMTL ID : 8w6r.1

murine SMPDL3A bound to sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: Y.329, N.331, T.333, E.334, S.388 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: G.42, N.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.44 NAG.3: 2 residues within 4Å: Chain A: N.213, W.217 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.213 NAG.4: 3 residues within 4Å: Chain A: Y.60, N.106, M.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.109 Hydrogen bonds: A:Y.60 Water bridges: A:N.106

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.85, N.126, H.227, H.268 Ligands: ZN.6, SO4.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.85, A:H.227, A:H.268, H2O.3 ZN.6: 6 residues within 4Å: Chain A: D.20, H.22, D.85, H.270 Ligands: ZN.5, SO4.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:H.22, A:D.85, A:H.270, H2O.3

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 9 residues within 4Å: Chain A: H.22, D.85, H.89, N.126, H.127, H.268, H.270 Ligands: ZN.5, ZN.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.126, A:H.268 Water bridges: A:Q.132, A:Y.189, A:Y.189 Salt bridges: A:H.22, A:H.89, A:H.127, A:H.268, A:H.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, Y. et al., SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Immunity (2023)

Release Date

2023-12-20

Peptides

Acid sphingomyelinase-like phosphodiesterase 3a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Acid sphingomyelinase-like phosphodiesterase 3a