SMTL ID : 7yxa.2 (1 other biounit)

XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: L.44, N.47, L.52, R.56 No protein-ligand interaction detected (PLIP)

1 x B2O: 4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid(Non-covalent)

B2O.2: 21 residues within 4Å: Chain A: Y.46, K.51, C.70, Y.116, N.119, I.120, W.135, R.138, E.139, V.142, F.143, V.212, L.213, P.214, W.380, L.383, D.405, L.408, G.409, A.411, M.412 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.116, A:Y.116, A:W.380, A:L.383, A:L.408, A:L.408 Hydrogen bonds: A:Y.46, A:Y.46, A:R.138 Salt bridges: A:K.51, A:E.139

2 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.3: 12 residues within 4Å: Chain A: V.229, L.232, A.233, C.236, A.237, A.240, R.241, V.377, G.381, F.384, L.385 Ligands: OLA.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.233, A:A.240 OLA.4: 2 residues within 4Å: Chain A: A.237 Ligands: OLA.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyapina, E. et al., Structural basis for receptor selectivity and inverse agonism in S1P 5 receptors. Nat Commun (2022)

Release Date

2022-08-10

Peptides

Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562

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