SMTL ID : 5tzr.1

GPR40 in complex with partial agonist MK-8666

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: F.339, S.342, N.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.342, A:S.342

1 x MK6: (5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid(Non-covalent)

MK6.2: 16 residues within 4Å: Chain A: P.93, A.96, V.97, F.100, Y.104, L.148, L.151, G.152, F.155, G.156, L.171, L.184, W.187, R.196, Y.415, R.433 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.93, A:V.97, A:V.97, A:F.100, A:L.151, A:L.151, A:F.155, A:F.155, A:W.187 Hydrogen bonds: A:Y.415 Water bridges: A:R.196 Salt bridges: A:R.196, A:R.433

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 4 residues within 4Å: Chain A: E.236, G.255, F.329, Q.330 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.245, A:D.245, A:R.370, A:R.370

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

OLC.4: 6 residues within 4Å: Chain A: P.194, F.197, S.198, L.201, F.423 Ligands: OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.194, A:F.197, A:L.201, A:L.201 OLC.5: 14 residues within 4Å: Chain A: P.53, Y.57, G.108, A.111, A.112, A.115, A.116, L.119, A.142, L.202, L.203, L.206, P.207, I.210 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.111, A:L.203, A:L.206, A:P.207, A:I.210 Hydrogen bonds: A:Y.57 OLC.6: 2 residues within 4Å: Chain A: V.26, A.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.26 OLC.7: 2 residues within 4Å: Chain A: F.197 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.197 OLC.8: 2 residues within 4Å: Ligands: OLC.4, OLC.7 No protein-ligand interaction detected (PLIP) OLC.9: 5 residues within 4Å: Chain A: F.215, L.395, A.398, W.399, G.402 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.215, A:L.395, A:A.398, A:W.399, A:W.399 OLC.10: 5 residues within 4Å: Chain A: Q.19, L.20, G.23, A.27, W.442 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20, A:A.27, A:W.442 OLC.11: 5 residues within 4Å: Chain A: L.74, V.77, P.86, L.87, L.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.74, A:L.87

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

1PE.12: 4 residues within 4Å: Chain A: A.417, V.420, Y.425, L.428 No protein-ligand interaction detected (PLIP) 1PE.13: 4 residues within 4Å: Chain A: K.360, S.361, R.362, N.365 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J. et al., Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-06-07

Peptides

Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1

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