SMTL ID : 9ct5.1

HsSTING with diABZI and C53, together conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

4 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.1: 17 residues within 4Å: Chain A: Y.46, L.49, H.50, S.53, Y.106, N.111, V.113, G.114, P.115, M.120, L.123, L.124 Chain B: Y.46, L.49, H.50, S.53, M.120 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.50, A:V.113, A:L.124, B:L.49 Hydrogen bonds: A:N.111 pi-Cation interactions: A:H.50 9IM.3: 17 residues within 4Å: Chain C: L.49, H.50, S.53, Y.106, V.113, G.114, P.115, M.120, L.123, L.124 Chain D: Y.46, L.49, H.50, S.53, Y.106, M.120, L.123 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:H.50, C:V.113, C:L.124, D:Y.46, D:L.49, D:L.123 pi-Cation interactions: C:H.50, C:H.50 Halogen bonds: C:S.53 Hydrogen bonds: D:Y.106 9IM.6: 15 residues within 4Å: Chain E: Y.46, L.49, H.50, S.53, Y.106, V.113, P.115, M.120, L.123, L.124 Chain F: Y.46, L.49, H.50, M.120, L.123 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.49, E:V.113, F:Y.46, F:L.49, F:L.49, F:H.50 Hydrogen bonds: E:Y.106, E:N.111 pi-Cation interactions: E:H.50 9IM.8: 15 residues within 4Å: Chain G: Y.46, H.50, S.53, N.111, V.113, P.115, M.120, L.123, L.124 Chain H: Y.46, L.49, H.50, S.53, M.120, L.123 11 PLIP interactions: 5 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:Y.46, H:L.49, H:H.50, H:L.123, G:H.50, G:V.113, G:L.124 pi-Stacking: H:H.50 Hydrogen bonds: G:N.111 pi-Cation interactions: G:H.50, G:H.50

4 x 01: 1-[(2E)-4-{5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-methoxy-1H-1,3-benzimidazol-1-yl}but-2-en-1-yl]-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-[3-(morpholin-4-yl)propoxy]-1H-1,3-benzimidazole-5-carboxamide

01.2: 21 residues within 4Å: Chain A: L.159, S.162, Y.163, G.166, Y.167, R.238, Y.240, S.241, T.263, P.264 Chain B: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.159, B:Y.163, A:L.159, A:Y.167, A:Y.240, A:P.264 Hydrogen bonds: B:S.241, B:S.241, B:T.263, A:R.238, A:S.241, A:S.241 pi-Stacking: B:Y.163, B:Y.167, A:Y.167 pi-Cation interactions: B:R.238 01.4: 20 residues within 4Å: Chain C: L.159, S.162, Y.163, G.166, Y.167, R.238, Y.240, S.241, E.260, T.263 Chain D: L.159, S.162, Y.163, G.166, Y.167, V.239, Y.240, S.241, T.263, P.264 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:Y.240, D:P.264, C:L.159, C:Y.240, C:Y.240 Hydrogen bonds: D:V.239, D:S.241, D:T.263, C:R.238, C:S.241, C:S.241, C:T.263 pi-Stacking: D:Y.163, D:Y.167, C:Y.167, C:Y.167 pi-Cation interactions: D:R.238 01.5: 21 residues within 4Å: Chain E: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 Chain F: L.159, S.162, Y.163, G.166, Y.167, V.239, Y.240, S.241, T.263, P.264 16 PLIP interactions: 9 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:L.159, E:Y.163, E:Y.240, F:L.159, F:Y.167, F:Y.240, F:P.264 Hydrogen bonds: E:R.238, E:S.241, E:S.241, E:T.263, F:S.241, F:S.241 pi-Stacking: E:Y.167, E:Y.167, F:Y.163 01.7: 20 residues within 4Å: Chain G: L.159, S.162, Y.163, G.166, Y.167, V.239, Y.240, S.241, T.263, P.264 Chain H: L.159, S.162, Y.163, G.166, Y.167, V.239, Y.240, S.241, T.263, P.264 13 PLIP interactions: 7 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:L.159, H:Y.167, H:P.264, G:L.159, G:Y.240 Hydrogen bonds: H:S.241, H:S.241, G:S.241, G:S.241, G:T.263 pi-Stacking: H:Y.163, H:Y.167, G:Y.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gharpure, A. et al., Distinct oligomeric assemblies of STING induced by non-nucleotide agonists. Nat Commun (2025)

Release Date

2025-04-23

Peptides

Stimulator of interferon genes protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

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

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