SMTL ID : 9cgk.1

CryoEM structure of delta opioid receptor bound to G proteins and a full bitopic agonist

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.62 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x 01: N-{5-[(4bS,8R,8aS,15bR)-1,8a-dihydroxy-5,6,8,8a,9,15b-hexahydro-7H-4,8-methano[1]benzofuro[3,2-c]pyrido[3,4-b]acridin-7-yl]pentyl}guanidine

01.1: 15 residues within 4Å: Chain A: A.63, D.93, Y.94, N.96, M.97, S.100, V.182, W.239, I.242, H.243, V.246, I.269, G.272, N.275, S.276 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.94, A:W.239, A:I.242, A:V.246, A:V.246, A:I.269 Hydrogen bonds: A:S.100, A:S.100, A:G.272, A:S.276 Salt bridges: A:D.93 pi-Stacking: A:H.243, A:W.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varga, B.R. et al., Structure-guided design of partial agonists at an opioid receptor. Nat Commun (2025)

Release Date

2025-04-02

Peptides

Delta-type opioid receptor: A
ScFv16 protein: B
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: C
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: D
Guanine nucleotide-binding protein G(i) subunit alpha-1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
D

D
C

E
B

Membrane

We predict this structure to be a membrane protein.
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Delta-type opioid receptor

ScFv16 protein

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(i) subunit alpha-1

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