SMTL ID : 6li0.1

Crystal structure of GPR52 in complex with agonist c17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x EN6: N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide(Non-covalent)

EN6.1: 24 residues within 4Å: Chain A: P.13, Y.19, S.20, D.23, V.24, C.25, E.28, T.29, I.32, C.79, L.86, F.102, Y.170, H.171, D.173, I.174, F.175, E.176, A.179, P.404, S.407, F.408, T.411, W.412 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.13, A:E.28, A:I.32, A:D.173, A:I.174, A:F.408, A:F.408, A:T.411, A:W.412 Hydrogen bonds: A:C.25, A:F.175, A:E.176 pi-Stacking: A:F.408

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: S.230, T.231, T.232, G.233, N.234, T.235, S.278, T.279, W.280, G.281, D.282, C.313, G.314, D.315, W.318, Y.320, F.321, C.322 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.280, A:W.280, A:W.318 Hydrogen bonds: A:T.231, A:T.232, A:T.232, A:N.234, A:N.234, A:T.235, A:S.278, A:T.279, A:T.279, A:W.280, A:D.315, A:Y.320, A:C.322 pi-Stacking: A:W.318, A:W.318

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

OLC.3: 5 residues within 4Å: Chain A: N.403, T.405, L.409 Ligands: OLC.5, OLC.8 Ligand excluded by PLIP OLC.4: 5 residues within 4Å: Chain A: R.377, M.384, P.388, L.406 Ligands: OLC.5 Ligand excluded by PLIP OLC.5: 7 residues within 4Å: Chain A: R.377, S.380, V.381, M.384, L.413 Ligands: OLC.3, OLC.4 Ligand excluded by PLIP OLC.6: 6 residues within 4Å: Chain A: A.198, F.202, C.205, F.206, F.209 Ligands: OLC.7 Ligand excluded by PLIP OLC.7: 3 residues within 4Å: Chain A: C.205 Ligands: OLC.6, OLC.15 Ligand excluded by PLIP OLC.8: 3 residues within 4Å: Chain A: G.15, T.405 Ligands: OLC.3 Ligand excluded by PLIP OLC.9: 3 residues within 4Å: Chain A: L.159, F.162, F.163 Ligand excluded by PLIP OLC.11: 9 residues within 4Å: Chain A: H.58, R.124, I.128, F.212, R.216, K.307, I.368, R.369, L.372 Ligand excluded by PLIP OLC.12: 7 residues within 4Å: Chain A: W.115, C.119, V.122, D.123, V.138, C.146 Ligands: OLC.13 Ligand excluded by PLIP OLC.13: 5 residues within 4Å: Chain A: W.115, C.146, L.149, Y.153 Ligands: OLC.12 Ligand excluded by PLIP OLC.15: 9 residues within 4Å: Chain A: V.193, A.201, V.204, C.205, F.376, S.380, Y.383, L.387 Ligands: OLC.7 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain A: R.377, I.424, S.428 Ligand excluded by PLIP OLC.17: 9 residues within 4Å: Chain A: L.14, F.16, G.17, H.18, V.24, C.25, I.26, F.27, E.28 Ligand excluded by PLIP OLC.18: 4 residues within 4Å: Chain A: L.156, P.160, F.163, W.165 Ligand excluded by PLIP OLC.19: 6 residues within 4Å: Chain A: L.38, G.42, T.45, F.419, V.423, A.426 Ligand excluded by PLIP OLC.20: 3 residues within 4Å: Chain A: L.44, T.45, F.48 Ligand excluded by PLIP OLC.21: 7 residues within 4Å: Chain A: F.27, V.31, L.38, L.385, W.412, S.416, C.420 Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 2 residues within 4Å: Chain A: G.164, W.165 No protein-ligand interaction detected (PLIP) PEG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.23: 2 residues within 4Å: Chain A: E.319, Y.320 No protein-ligand interaction detected (PLIP) PEG.24: 3 residues within 4Å: Chain A: D.326, R.345, R.438 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.438 PEG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.26: 6 residues within 4Å: Chain A: N.135, F.270, D.271, Q.304, G.305, R.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.135, A:D.271 PEG.27: 2 residues within 4Å: Chain A: S.398, R.399 No protein-ligand interaction detected (PLIP) PEG.28: 5 residues within 4Å: Chain A: Q.217, H.218, T.219, K.220, E.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:T.219

1 x FLC: CITRATE ANION(Non-covalent)

FLC.14: 5 residues within 4Å: Chain A: G.366, R.369, R.370, M.373, R.377 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.369, A:R.369 Salt bridges: A:R.369, A:R.369, A:R.370, A:R.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, X. et al., Structural basis of ligand recognition and self-activation of orphan GPR52. Nature (2020)

Release Date

2020-02-26

Peptides

Chimera of G-protein coupled receptor 52 and Flavodoxin: 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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Chimera of G-protein coupled receptor 52 and Flavodoxin