SMTL ID : 8w6p.1

Crystal structure of dimeric murine SMPDL3A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 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: 9 residues within 4Å: Chain A: E.324, K.328, N.332, T.334 Chain B: K.141, L.144, G.145, E.146, I.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.141 NAG-NAG.3: 6 residues within 4Å: Chain A: Y.319, N.321, T.323, E.324, S.378 Chain B: Q.102 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 5 residues within 4Å: Chain A: N.200, N.203, S.204, W.207, N.208 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.203, A:N.203, A:N.208 Hydrophobic interactions: A:W.207 Hydrogen bonds: A:S.204

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 5 residues within 4Å: Chain B: Y.319, N.321, T.323, E.324, S.378 No protein-ligand interaction detected (PLIP)

1 x YA4: [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid(Non-covalent)

YA4.5: 10 residues within 4Å: Chain A: H.12, D.75, H.79, N.116, H.117, H.258, T.259, H.260 Ligands: ZN.8, ZN.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.75 Water bridges: A:D.75, A:N.116

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.6: 3 residues within 4Å: Chain A: T.24, G.32, N.34 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.24 Hydrogen bonds: A:N.34 Water bridges: A:T.24 NAG.7: 3 residues within 4Å: Chain A: Y.50, N.96, M.99 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.99 Hydrogen bonds: A:N.96 Water bridges: A:P.15 NAG.10: 1 residues within 4Å: Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: T.24, G.32, N.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.34 NAG.13: 4 residues within 4Å: Chain B: N.200, N.203, W.207 Ligands: FUC.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.203, B:N.203 NAG.14: 4 residues within 4Å: Chain B: Y.50, N.96, M.99 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.99 Water bridges: B:N.96, B:N.96, B:N.96, B:T.100

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: D.75, N.116, H.217, H.258 Ligands: YA4.5, ZN.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.75, A:H.217, A:H.258, H2O.2 ZN.9: 6 residues within 4Å: Chain A: D.10, H.12, D.75, H.260 Ligands: YA4.5, ZN.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:H.12, A:D.75, A:H.260, H2O.2 ZN.16: 6 residues within 4Å: Chain B: D.10, H.12, D.75, H.260 Ligands: PO4.15, ZN.17 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:H.12, B:D.75, B:H.260, H2O.17 ZN.17: 7 residues within 4Å: Chain B: D.10, D.75, N.116, H.217, H.258 Ligands: PO4.15, ZN.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.75, B:H.217, B:H.258, H2O.17

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.11: 3 residues within 4Å: Chain B: S.204, N.208 Ligands: NAG.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.208, B:N.208

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 9 residues within 4Å: Chain B: H.12, D.75, H.79, N.116, H.117, H.258, H.260 Ligands: ZN.16, ZN.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.75, B:N.116, B:H.258 Water bridges: B:D.75, B:D.75, B:H.79, B:H.117 Salt bridges: B:H.79, B:H.117, B:H.258, B:H.260

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acid sphingomyelinase-like phosphodiesterase 3a