SMTL ID : 6li2.1

Crystal structure of GPR52 ligand free form with rubredoxin fusion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.226, C.229, C.259, C.262 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.229, A:C.259, A:C.262

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

OLC.2: 6 residues within 4Å: Chain A: F.280, S.284, V.285, M.288, L.289 Ligands: OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.288, A:L.289 OLC.3: 4 residues within 4Å: Chain A: V.285, V.327, I.328, L.331 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.285 Hydrogen bonds: A:L.331 OLC.4: 5 residues within 4Å: Chain A: V.22, V.24, I.26, T.29, H.88 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.26, A:T.29 Hydrogen bonds: A:V.22 Salt bridges: A:H.88 OLC.5: 4 residues within 4Å: Chain A: R.337, L.340, R.341, S.344 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.340, A:R.341 Hydrogen bonds: A:L.340 OLC.6: 7 residues within 4Å: Chain A: T.45, V.49, T.335, F.336, G.339, L.340 Ligands: OLC.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.45, A:L.340 Hydrogen bonds: A:T.335 OLC.7: 4 residues within 4Å: Chain A: T.45, V.49 Ligands: OLC.6, OLC.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.45 Hydrogen bonds: A:V.49 OLC.8: 2 residues within 4Å: Chain A: L.343 Ligands: OLC.7 No protein-ligand interaction detected (PLIP) OLC.9: 1 residues within 4Å: Ligands: OLC.10 No protein-ligand interaction detected (PLIP) OLC.10: 7 residues within 4Å: Chain A: P.160, W.165, Y.187, F.191, C.194, L.195 Ligands: OLC.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.191, A:L.195 OLC.11: 5 residues within 4Å: Chain A: G.15, H.18, Y.19, D.23, F.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.23 Salt bridges: A:H.18 OLC.12: 6 residues within 4Å: Chain A: N.307, T.309, L.310, L.313, T.314 Ligands: OLC.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.313, A:L.313, A:T.314 Hydrogen bonds: A:N.307

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

PEG.13: 3 residues within 4Å: Chain A: R.9, E.176, S.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.9, A:S.181, A:S.181

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 Rubredoxin: 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 Rubredoxin