SMTL ID : 6rnk.1

Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a nanobody and antagonist NF-56-EJ40.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-mer

Ligands

1 x KAZ: 2-[2-[[3-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]phenyl]carbonylamino]phenyl]ethanoic acid(Non-covalent)

KAZ.1: 17 residues within 4Å: Chain A: E.25, Y.33, L.82, S.85, Y.86, G.89, N.90, W.91, N.101, R.102, L.105, H.106, C.175, Y.251, R.283, F.287 Ligands: GOL.15 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.82, A:Y.86, A:Y.86, A:W.91, A:W.91, A:W.91, A:N.101, A:R.102, A:L.105, A:Y.251, A:F.287 Hydrogen bonds: A:Y.33, A:R.102 Water bridges: A:W.91, A:H.106 Salt bridges: A:E.25, A:E.25, A:R.283 pi-Cation interactions: A:R.102

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

OLC.2: 15 residues within 4Å: Chain A: S.60, Y.64, F.118, I.121, D.122, L.125, L.136, Q.137, F.141, I.145, A.148, V.149, L.152 Ligands: OLC.3, OLC.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.118, A:F.118, A:L.136, A:A.148, A:L.152 Hydrogen bonds: A:Y.64, A:F.118, A:D.122, A:D.122 Water bridges: A:S.60 OLC.3: 8 residues within 4Å: Chain A: L.114, I.121, Y.124, K.128, L.136, F.208, F.209 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.114, A:I.121, A:I.121 Hydrogen bonds: A:Y.124 Water bridges: A:K.212 OLC.4: 7 residues within 4Å: Chain A: W.58, R.132, I.135, K.138, K.139, E.140 Chain B: T.118 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.135, A:K.138, A:K.138 Hydrogen bonds: A:K.139 OLC.5: 7 residues within 4Å: Chain A: F.163, Y.178, G.182, N.183, Y.186, S.187, Y.190 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.163, A:F.163, A:Y.178, A:Y.186, A:Y.186, A:Y.190, A:Y.190 Hydrogen bonds: A:N.183, A:S.187 OLC.6: 9 residues within 4Å: Chain A: K.56, W.58, F.66, N.67, K.139, I.143, S.146, W.150 Ligands: OLC.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.58, A:F.66, A:W.150, A:W.150 Hydrogen bonds: A:W.58, A:W.58, A:K.139 Salt bridges: A:K.139 OLC.7: 6 residues within 4Å: Chain A: A.74, T.78, M.81, L.97, S.100, N.101 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.74 Hydrogen bonds: A:N.101 OLC.8: 7 residues within 4Å: Chain A: I.201, S.204, V.205, C.207, F.208, Y.211 Ligands: OLC.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.201, A:V.205, A:F.208 OLC.9: 5 residues within 4Å: Chain A: L.52, M.55, W.58, F.66 Ligands: OLC.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.55 OLC.10: 5 residues within 4Å: Chain A: L.192, F.199, I.253, N.256, V.257 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.199, A:I.253 OLC.11: 4 residues within 4Å: Chain A: I.189, L.192, C.193, L.196 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.196 OLC.12: 9 residues within 4Å: Chain A: Y.28, F.32, I.253, M.254, V.257, L.278, L.281, T.282, L.285 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.32, A:L.285, A:L.285 OLC.13: 5 residues within 4Å: Chain A: W.17, C.270, A.274, L.278, L.281 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.17, A:W.17, A:A.274, A:L.278, A:L.278, A:L.281 OLC.14: 11 residues within 4Å: Chain A: Y.93, G.94, D.95, V.96, L.97, S.100, Y.103, V.104, T.154, L.158, L.161 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.96, A:L.97, A:V.104, A:T.154, A:L.158, A:L.161 Hydrogen bonds: A:G.94, A:D.95, A:V.96, A:L.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: Y.86, R.102, C.175, D.177, R.283 Ligands: KAZ.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.86, A:R.102, A:R.102, A:C.175, A:D.177, A:D.177 Water bridges: A:R.283

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.16: 3 residues within 4Å: Chain A: H.134, I.135, L.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.135, A:L.136 Salt bridges: A:H.134

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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