SMTL ID : 9ct6.1

HsSTING with diABZI and C53, apart conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

6 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

01.1: 22 residues within 4Å: Chain A: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, 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 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.159, A:Y.163, A:Y.167, A:Y.240, A:Y.240, B:L.159 Hydrogen bonds: A:R.238, A:S.241, A:S.241, A:T.263, B:S.241, B:S.241, B:T.263 pi-Stacking: A:Y.167, B:Y.163, B:Y.167, B: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, V.239, Y.240, S.241, T.263, P.264 Chain D: L.159, S.162, G.166, Y.167, R.238, Y.240, S.241, T.263, P.264 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.159, C:Y.240, D:L.159, D:Y.167, D:Y.240, D:P.264 Hydrogen bonds: C:R.238, C:R.238, C:S.241, C:S.241, C:T.263, D:S.241 pi-Stacking: C:Y.167, C:Y.167, D:Y.167 pi-Cation interactions: C:R.238 01.5: 19 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, Y.240, T.263, P.264 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:L.159, E:Y.240, F:L.159, F:Y.167, F:Y.240 Hydrogen bonds: E:S.241, E:S.241, E:T.263, F:Y.167 pi-Stacking: E:Y.167, E:Y.167, F:Y.163 01.7: 21 residues within 4Å: Chain G: L.159, S.162, Y.163, G.166, Y.167, R.238, Y.240, S.241, T.263, P.264 Chain H: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 19 PLIP interactions: 10 interactions with chain G, 9 interactions with chain H Hydrophobic interactions: G:L.159, G:Y.167, G:Y.240, G:Y.240, H:L.159, H:Y.163, H:Y.167, H:Y.240, H:P.264 Hydrogen bonds: G:R.238, G:S.241, G:S.241, G:T.263, H:S.241, H:S.241, H:T.263 pi-Stacking: G:Y.163, G:Y.167 pi-Cation interactions: H:R.238 01.9: 23 residues within 4Å: Chain I: L.159, S.162, Y.163, G.166, Y.167, R.238, Y.240, S.241, N.242, E.260, T.263, P.264 Chain J: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 17 PLIP interactions: 8 interactions with chain J, 9 interactions with chain I Hydrophobic interactions: J:L.159, J:Y.240, I:Y.163, I:Y.167, I:Y.240, I:Y.240 Hydrogen bonds: J:S.241, J:S.241, J:T.263, I:R.238, I:S.241, I:S.241, I:N.242 pi-Stacking: J:Y.167, J:Y.167, I:Y.167 pi-Cation interactions: J:R.238 01.11: 22 residues within 4Å: Chain K: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 Chain L: L.159, S.162, Y.163, G.166, Y.167, R.238, V.239, Y.240, S.241, T.263, P.264 15 PLIP interactions: 9 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:L.159, K:Y.163, K:Y.240, K:P.264, L:L.159, L:Y.167, L:P.264 Hydrogen bonds: K:V.239, K:S.241, K:T.263, L:R.238, L:S.241 pi-Stacking: K:Y.167, K:Y.167, L:Y.163

6 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.2: 16 residues within 4Å: Chain A: Y.46, L.49, H.50, S.53, Y.106, N.111, V.113, P.115, M.120, L.123, L.124 Chain B: Y.46, L.49, H.50, S.53, M.120 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.46, B:L.49, B:H.50, A:V.113, A:V.113, A:P.115, A:L.124 pi-Cation interactions: B:H.50, A:H.50, A:H.50 Hydrogen bonds: A:S.53, A:N.111 9IM.3: 18 residues within 4Å: Chain C: Y.46, L.49, H.50, S.53, N.111, V.113, P.115, M.120, L.123, L.124, S.127 Chain D: Y.46, L.49, H.50, S.53, M.120, L.123, L.124 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:Y.46, D:L.49, D:L.49, D:H.50, D:L.124, C:L.49, C:H.50, C:V.113, C:L.124 Hydrogen bonds: C:N.111 pi-Stacking: C:H.50, C:H.50 Halogen bonds: C:S.127 9IM.6: 16 residues within 4Å: Chain E: Y.46, L.49, H.50, S.53, N.111, V.113, P.115, M.120, L.123, L.124 Chain F: Y.46, L.49, H.50, S.53, M.120, L.123 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Y.46, E:Y.46, E:V.113, E:L.124, F:L.49, F:L.49 Hydrogen bonds: E:N.111 pi-Stacking: E:H.50, E:H.50 9IM.8: 17 residues within 4Å: Chain G: 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 H: Y.46, L.49, H.50, S.53, M.120 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:Y.46, G:H.50, G:V.113, G:L.124, H:L.49, H:L.49 Hydrogen bonds: G:N.111 pi-Stacking: G:H.50, G:H.50 9IM.10: 15 residues within 4Å: Chain I: Y.46, L.49, H.50, S.53, V.113, P.115, M.120, L.123, L.124 Chain J: Y.46, L.49, H.50, S.53, M.120, L.123 10 PLIP interactions: 7 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:H.50, I:V.113, I:P.115, I:L.124, J:L.49, J:L.49 Hydrogen bonds: I:S.53 pi-Cation interactions: I:H.50, I:H.50, J:H.50 9IM.12: 17 residues within 4Å: Chain K: Y.46, L.49, H.50, S.53, Y.106, N.111, V.113, P.115, M.120, L.123, L.124 Chain L: L.49, H.50, S.53, Y.106, M.120, L.124 12 PLIP interactions: 7 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:Y.46, K:L.49, K:V.113, K:L.124, L:L.49, L:L.49, L:H.50 Hydrogen bonds: K:Y.106, K:N.111 pi-Stacking: K:H.50 pi-Cation interactions: L:H.50 Halogen bonds: L:Y.106

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Membrane

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

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