SMTL ID : 8flm.1

Cryo-EM structure of STING oligomer bound to cGAMP, NVS-STG2 and C53

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

2 x Y6H: 4-({[4-(2-tert-butyl-5,5-dimethyl-1,3-dioxan-2-yl)phenyl]methyl}amino)-3-methoxybenzoic acid(Non-covalent)

Y6H.1: 21 residues within 4Å: Chain A: V.48, L.51, A.52, Q.55, R.94, R.95, L.98, L.101, S.102, F.105 Chain B: L.130, L.134, L.136 Chain C: L.44, L.47, V.48, L.51 Chain D: L.130, L.134, L.136 Ligands: Y6H.4 11 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: A:L.51, A:L.51, A:A.52, A:L.98, A:L.98, B:L.136, B:L.136, D:L.130, C:L.44 Hydrogen bonds: A:Q.55 Salt bridges: A:R.95 Y6H.4: 21 residues within 4Å: Chain A: L.44, L.47, V.48, L.51 Chain B: L.130, L.134, L.136 Chain C: V.48, L.51, A.52, Q.55, R.94, R.95, L.98, L.101, S.102, F.105 Chain D: L.130, L.134, L.136 Ligands: Y6H.1 12 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:V.48, C:L.51, C:A.52, C:Q.55, C:L.98, C:L.98, D:L.136, D:L.136, B:L.130 Hydrogen bonds: C:Q.55, C:R.94 Salt bridges: C:R.95

2 x 1SY: cGAMP(Non-covalent)

1SY.2: 27 residues within 4Å: Chain A: S.162, Y.163, G.166, Y.167, R.232, I.235, R.238, Y.240, E.260, Y.261, T.263, P.264, T.267 Chain B: S.162, Y.163, G.166, Y.167, R.232, I.235, R.238, V.239, Y.240, S.241, E.260, T.263, P.264, T.267 23 PLIP interactions: 14 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.162, A:S.162, A:R.232, A:R.238, A:T.263, A:T.263, A:T.263, A:T.267, B:R.238, B:R.238, B:V.239, B:T.267 Salt bridges: A:R.238, A:E.260, B:R.232, B:R.238 pi-Stacking: A:Y.167, B:Y.167 pi-Cation interactions: A:Y.167, A:R.238, A:R.238, B:R.238, B:R.238 1SY.6: 27 residues within 4Å: Chain C: S.162, Y.163, G.166, Y.167, R.232, I.235, R.238, Y.240, E.260, Y.261, T.263, P.264, T.267 Chain D: S.162, Y.163, G.166, Y.167, R.232, I.235, R.238, V.239, Y.240, S.241, E.260, T.263, P.264, T.267 20 PLIP interactions: 11 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.162, C:S.162, C:R.232, C:R.238, C:T.263, C:T.267, D:R.238, D:R.238, D:V.239, D:T.267 Salt bridges: C:R.238, C:E.260, D:R.232, D:R.238 pi-Stacking: C:Y.167, D:Y.167 pi-Cation interactions: C:Y.167, C:R.238, D:R.238, D:R.238

2 x 9IM: 1-[(2-chloro-6-fluorophenyl)methyl]-3,3-dimethyl-2-oxo-N-[(2,4,6-trifluorophenyl)methyl]-2,3-dihydro-1H-indole-6-carboxamide(Non-covalent)

9IM.3: 19 residues within 4Å: Chain A: Y.46, L.47, L.49, H.50, S.53, Y.106, M.120, L.123, L.124 Chain B: Y.46, L.47, L.49, H.50, S.53, Y.106, W.119, M.120, L.123, L.124 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.46, A:L.49, A:L.124, B:L.49, B:L.123 pi-Cation interactions: A:H.50 pi-Stacking: B:H.50 9IM.5: 19 residues within 4Å: Chain C: Y.46, L.47, L.49, H.50, S.53, Y.106, M.120, L.123, L.124 Chain D: Y.46, L.47, L.49, H.50, S.53, Y.106, W.119, M.120, L.123, L.124 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.49, C:Y.46, C:L.49, C:L.124 pi-Stacking: D:H.50 Hydrogen bonds: C:Y.106 pi-Cation interactions: C:H.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Activation of human STING by a molecular glue-like compound. Nat.Chem.Biol. (2024)

Release Date

2023-11-01

Peptides

Stimulator of interferon genes protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Stimulator of interferon genes protein

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