SMTL ID : 7ljd.1

Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in complex with miniGs protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x LDP: L-DOPAMINE(Non-covalent)

LDP.1: 10 residues within 4Å: Chain A: D.151, S.155, T.156, L.238, S.246, S.250, F.336, F.337, N.340, W.369 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.336 Hydrogen bonds: A:S.155, A:S.246, A:S.246, A:S.250, A:S.250, A:N.340, A:W.369 pi-Stacking: A:F.337

1 x G4C: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone(Non-covalent)

G4C.2: 8 residues within 4Å: Chain A: W.171, S.175, R.178, K.182, M.183, K.186, A.187, I.190 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:W.171, A:R.178, A:A.187, A:I.190 Hydrogen bonds: A:R.178, A:K.186 pi-Stacking: A:W.171 pi-Cation interactions: A:R.178

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 4 residues within 4Å: Chain A: R.240, T.241, I.244, I.249 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.240, A:I.244, A:I.249 CLR.4: 3 residues within 4Å: Chain A: R.71, I.72, S.79 No protein-ligand interaction detected (PLIP) CLR.5: 6 residues within 4Å: Chain A: T.316, L.319, K.320, S.323, V.324, V.328 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.316, A:L.319, A:K.320, A:V.324 CLR.6: 3 residues within 4Å: Chain A: V.200, Q.208, L.209 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.200, A:Q.208, A:L.209 CLR.7: 5 residues within 4Å: Chain A: K.186, F.189, I.190, S.193, V.194 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.189, A:I.190, A:V.194

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.8: 6 residues within 4Å: Chain A: L.78, E.133, N.359, V.363, W.366, A.370 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.78, A:V.363, A:A.370 PLM.9: 4 residues within 4Å: Chain A: V.123, L.124, W.128, F.140 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.123, A:L.124, A:W.128, A:F.140, A:F.140, A:F.140 PLM.10: 4 residues within 4Å: Chain A: F.140, S.142, F.143, F.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.140, A:F.140, A:F.143 Hydrogen bonds: A:S.142, A:S.142 PLM.11: 6 residues within 4Å: Chain A: F.109, I.112, F.189, I.192, W.196, F.204 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.112, A:I.112, A:F.189, A:I.192, A:I.192, A:W.196, A:W.196, A:F.204 Salt bridges: A:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhuang, Y. et al., Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor. Cell Res. (2021)

Release Date

2021-03-03

Peptides

D(1A) dopamine receptor: A
Engineered Gs protein alpha subunit: 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
Nanobody 35: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
B

D
G

E
N

Membrane

We predict this structure to be a membrane protein.
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D(1A) dopamine receptor

Engineered Gs protein alpha subunit

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

Nanobody 35

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