SMTL ID : 8f7w.1

Gi bound kappa-opioid receptor in complex with dynorphin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x TYR- GLY- GLY- PHE- LEU- ARG- ARG- ILE: Dynorphin(Non-covalent)

TYR-GLY-GLY-PHE-LEU-ARG-ARG-ILE.1: 20 residues within 4Å: Chain A: T.109, Q.113, V.132, I.133, D.136, Y.137, M.140, K.198, E.207, C.208, Y.217, V.228, I.292, E.295, H.302, A.306, L.307, Y.310, I.314, Y.318 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.109, A:Q.113, A:V.132, A:I.133, A:Y.137, A:V.228, A:I.292 Hydrogen bonds: A:Q.113, A:D.136, A:Y.137, A:K.198 Salt bridges: A:E.207, A:D.214, A:E.295 pi-Cation interactions: A:Y.217, A:Y.310

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 7 residues within 4Å: Chain A: L.72, M.79, I.83, F.97, L.101, A.104, T.108 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.72, A:F.97, A:L.101 CLR.3: 4 residues within 4Å: Chain A: V.283, T.286, P.287, F.291 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.283, A:T.286, A:P.287, A:F.291, A:F.291 CLR.4: 3 residues within 4Å: Chain A: T.245, L.249, V.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.249, A:V.282

2 x PLM: PALMITIC ACID(Non-functional Binders)(Non-covalent)

PLM.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PLM.6: 3 residues within 4Å: Chain A: M.149, K.172, L.183 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structures of the entire human opioid receptor family. Cell (2023)

Release Date

2022-12-14

Peptides

Kappa-type opioid receptor: A
Guanine nucleotide-binding protein G(i) subunit alpha-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
scFv16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
B

D
C

E
E

Membrane

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

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

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

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

scFv16

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