SMTL ID : 8s4d.1

Crystal structure of a peptidergic GPCR in complex with a small synthetic G protein-biased agonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

1 x 01: (3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid

01.1: 17 residues within 4Å: Chain A: F.96, W.103, S.124, I.127, F.128, R.186, M.201, Y.203, W.379, Y.382, K.386, Y.389, M.406, F.409, T.413, Y.417 Ligands: OLA.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.103, A:Y.389, A:Y.389, A:Y.389, A:F.409, A:F.409, A:F.409, A:F.409, A:F.409, A:Y.417

6 x OLA: OLEIC ACID(Non-covalent)

OLA.2: 14 residues within 4Å: Chain A: F.128, Y.132, L.177, L.178, P.181, V.182, R.186, M.201, Y.203, L.219, S.222, S.223, K.386 Ligands: 01.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.128, A:F.128, A:L.178, A:V.182, A:L.219 Salt bridges: A:R.186 OLA.3: 8 residues within 4Å: Chain A: F.85, F.136, F.143, D.144, L.160, A.167, V.230, I.234 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.85, A:F.136, A:F.143, A:A.167, A:V.230, A:I.234 OLA.4: 4 residues within 4Å: Chain A: V.369, V.370, V.373 Ligands: OLA.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.369 OLA.5: 5 residues within 4Å: Chain A: V.370, L.426, F.429, F.430 Ligands: OLA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.370, A:L.426, A:F.429, A:F.429, A:F.430 OLA.6: 5 residues within 4Å: Chain A: A.214, W.215, G.218, L.219, S.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.215, A:W.215, A:L.219, A:L.219 OLA.7: 3 residues within 4Å: Chain A: V.91, T.95, W.172 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.91, A:T.95, A:W.172, A:W.172, A:W.172

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 5 residues within 4Å: Chain A: N.64, I.86, L.141, N.423, Y.427 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.86, A:L.141 Hydrogen bonds: A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, T.L. et al., Structural and functional determination of peptide versus small molecule ligand binding at the apelin receptor. Nat Commun (2024)

Release Date

2024-12-04

Peptides

Apelin receptor,Soluble cytochrome b562: 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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Apelin receptor,Soluble cytochrome b562