SMTL ID : 8tf5.1

Crystal structure of orphan G protein-coupled receptor 6, pseudoapo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.1: 9 residues within 4Å: Chain A: V.133, D.134, L.137, T.150, G.153, V.154, L.156, L.157 Ligands: OLA.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.157 Hydrogen bonds: A:D.134 Water bridges: A:D.134 OLC.2: 12 residues within 4Å: Chain A: L.129, V.133, Y.136, L.137, R.149, A.202, M.205, V.206, I.209, L.213 Ligands: OLA.13, OLA.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.129, A:V.133, A:A.202, A:M.205, A:V.206, A:I.209 Hydrogen bonds: A:R.149, A:R.149 OLC.11: 7 residues within 4Å: Chain A: A.353, C.354, P.370, Y.373, A.376, T.377, P.380 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.376, A:T.377, A:P.380 OLC.12: 10 residues within 4Å: Chain A: V.104, P.105, S.106, L.112, G.115, F.116, L.170, V.173 Ligands: OLA.17, CLR.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.112, A:L.170, A:V.173 Hydrogen bonds: A:P.105 OLC.14: 3 residues within 4Å: Chain A: A.60, L.406 Ligands: OLA.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.60

2 x P15: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL(Non-covalent)

P15.3: 15 residues within 4Å: Chain A: L.128, T.132, R.135, L.139, M.210, G.340, T.343, L.344, V.347, L.348, F.351, N.384, N.388, I.391, Y.392 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:N.384, A:N.384, A:Y.392 P15.5: 2 residues within 4Å: Chain A: Q.400, W.404 No protein-ligand interaction detected (PLIP)

12 x OLA: OLEIC ACID(Non-covalent)

OLA.4: 5 residues within 4Å: Chain A: A.197, A.201, F.204, F.207, V.363 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.197, A:F.207, A:V.363 OLA.6: 4 residues within 4Å: Chain A: L.170, L.174, G.175 Ligands: OLA.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.170, A:L.174, A:L.174 OLA.7: 3 residues within 4Å: Chain A: G.175, W.176 Ligands: OLA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.176, A:W.176, A:W.176 Water bridges: A:N.177, A:S.194 OLA.8: 9 residues within 4Å: Chain A: V.63, A.67, R.73, T.85, L.92, L.96, F.116 Ligands: OLA.17, CLR.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.63, A:A.67, A:T.85, A:L.92, A:F.116 Salt bridges: A:R.73 OLA.9: 6 residues within 4Å: Chain A: N.42, P.43, W.44, L.47, V.372 Ligands: OLA.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.43, A:W.44, A:W.44, A:L.47 Hydrogen bonds: A:N.42 OLA.10: 16 residues within 4Å: Chain A: H.97, L.117, V.187, V.188, R.189, V.196, L.199, S.200, W.355, F.358, C.362, A.371, T.374, Y.375, L.378 Ligands: OLA.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.117, A:V.188, A:V.196, A:L.199, A:W.355, A:F.358, A:T.374, A:Y.375 Hydrogen bonds: A:R.189 Water bridges: A:R.189 OLA.13: 9 residues within 4Å: Chain A: A.122, V.125, S.126, T.161, V.164, A.202, F.203 Ligands: OLC.2, OLA.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.125, A:T.161, A:V.164, A:A.202, A:F.203 OLA.15: 5 residues within 4Å: Chain A: Y.136, I.209, H.212, R.216 Ligands: OLC.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.209 Hydrogen bonds: A:Y.136 Salt bridges: A:H.212, A:R.216 OLA.16: 6 residues within 4Å: Chain A: L.156, A.159, A.160, T.163, V.164 Ligands: OLC.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.156, A:A.159, A:T.163, A:V.164 OLA.17: 6 residues within 4Å: Chain A: L.92, L.96, F.100, V.104 Ligands: OLA.8, OLC.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.92, A:L.96, A:F.100, A:V.104 OLA.18: 4 residues within 4Å: Chain A: P.43, L.47, V.50 Ligands: OLA.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.43, A:L.47, A:V.50 OLA.19: 4 residues within 4Å: Chain A: L.61, L.406, L.407 Ligands: OLC.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.406, A:L.406

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.20: 12 residues within 4Å: Chain A: V.78, G.81, S.82, T.85, L.89, F.116, A.119, S.120, W.162, L.166 Ligands: OLA.8, OLC.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.85, A:F.116, A:F.116, A:W.162, A:W.162, A:L.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barekatain, M. et al., Structural insights into the high basal activity and inverse agonism of the orphan receptor GPR6 implicated in Parkinson's disease. Sci.Signal. (2024)

Release Date

2024-12-04

Peptides

G-protein coupled receptor 6,Soluble cytochrome b562 chimera,Soluble cytochrome b562,G-protein coupled receptor 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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G-protein coupled receptor 6,Soluble cytochrome b562 chimera,Soluble cytochrome b562,G-protein coupled receptor 6