SMTL ID : 7yxa.1 (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: 8 residues within 4Å: Chain A: R.34, P.35, A.36, P.37, V.43, N.47, L.52, R.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47

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: 23 residues within 4Å: Chain A: Y.46, K.51, R.64, 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 Ligands: OLC.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.116, A:V.142, A:L.213, A:L.383, A:D.405, A:L.408 Hydrogen bonds: A:Y.46, A:W.135 Salt bridges: A:K.51, A:R.138, A:E.139

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

OLC.3: 9 residues within 4Å: Chain A: V.73, Q.403, D.405, P.406, G.409, L.410, M.412, A.413 Ligands: B2O.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.406, A:A.413 OLC.4: 15 residues within 4Å: Chain A: L.85, L.88, G.89, F.94, H.95, A.96, F.99, L.100, G.103, S.104, L.107, L.179, A.182, A.183, W.186 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.100, A:L.107, A:A.182, A:W.186, A:W.186 Hydrogen bonds: A:F.94 OLC.5: 8 residues within 4Å: Chain A: R.175, G.176, L.179, A.180, A.183, G.187, L.190, L.191 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.183

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
A

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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