SMTL ID : 6ibb.1 (1 other biounit)

Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

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

OLC.1: 3 residues within 4Å: Chain A: Y.27, Y.28, A.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.28, A:A.31 OLC.2: 4 residues within 4Å: Chain A: L.192, T.195, I.253, N.256 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.195, A:I.253 OLC.3: 8 residues within 4Å: Chain A: V.39, G.43, T.46, A.291, I.295, F.298, R.305 Ligands: H95.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.39, A:I.295, A:F.298, A:F.298, A:R.305 Hydrogen bonds: A:R.305 Salt bridges: A:R.305 OLC.4: 9 residues within 4Å: Chain A: I.99, R.102, Y.103, W.150, V.157, L.158, M.160, L.161 Ligands: OLC.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.103, A:W.150, A:L.158 Hydrogen bonds: A:I.99 OLC.5: 7 residues within 4Å: Chain A: M.41, F.45, C.77, M.81, T.92, Y.93, L.97 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.45 Hydrogen bonds: A:T.92 OLC.6: 9 residues within 4Å: Chain A: W.17, P.250, I.253, M.254, C.270, S.271, A.274, I.275, L.278 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.250, A:A.274, A:I.275, A:L.278 Hydrogen bonds: A:W.17 OLC.7: 12 residues within 4Å: Chain A: M.55, K.56, N.57, W.58, V.63, N.67, I.70, K.139, I.143, L.147, W.150 Ligands: OLC.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.70, A:I.143, A:W.150, A:W.150, A:W.150 Hydrogen bonds: A:M.55, A:K.56, A:W.58 Salt bridges: A:K.139 OLC.8: 10 residues within 4Å: Chain A: T.162, F.163, T.165, G.182, N.183, Y.186, I.189, Y.190, C.193, L.197 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.162, A:F.163, A:I.189, A:Y.190, A:L.197 Hydrogen bonds: A:N.183

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: E.21, K.25, V.176, D.177, S.180, K.276, I.280, R.283 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.177, A:S.180, A:S.180, A:K.276, A:R.283, A:R.283 Water bridges: A:K.25, A:D.177

1 x H95: (2~{S},5~{R})-hexane-2,5-diol(Non-covalent)

H95.10: 11 residues within 4Å: Chain A: K.232, R.235, F.298, L.299, G.301, D.302, H.303, F.304, R.305, D.306 Ligands: OLC.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.305 Hydrogen bonds: A:K.232, A:K.232, A:R.235, A:R.235, A:R.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haffke, M. et al., Structural basis of species-selective antagonist binding to the succinate receptor. Nature (2019)

Release Date

2019-08-14

Peptides

Succinate receptor 1: A
Nanobody6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Succinate receptor 1

Nanobody6

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