SMTL ID : 8ayn.1

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

4 x ZK1: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid(Non-covalent)

ZK1.1: 12 residues within 4Å: Chain A: E.423, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, E.726, M.729, Y.753 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.471 Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:S.675, A:S.675, A:S.675 pi-Stacking: A:Y.471 Halogen bonds: A:Y.471, A:Y.753 ZK1.11: 11 residues within 4Å: Chain D: E.423, Y.471, P.499, L.500, T.501, G.674, S.675, T.707, T.728, M.729, Y.753 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.471 Hydrogen bonds: D:P.499, D:T.501, D:S.675, D:S.675, D:S.675 pi-Stacking: D:Y.471 Halogen bonds: D:Y.471, D:T.728, D:Y.753 ZK1.15: 12 residues within 4Å: Chain E: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.708, M.730, Y.754 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.472, E:Y.472 Hydrogen bonds: E:P.500, E:T.502, E:R.507, E:R.507, E:S.676, E:S.676, E:S.676 pi-Stacking: E:Y.472 Halogen bonds: E:Y.754 ZK1.22: 12 residues within 4Å: Chain F: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.708, M.730, Y.754 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.472, F:Y.472 Hydrogen bonds: F:P.500, F:T.502, F:R.507, F:R.507, F:S.676, F:S.676, F:S.676 pi-Stacking: F:Y.472 Halogen bonds: F:Y.754

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

OLC.2: 7 residues within 4Å: Chain A: F.536, Y.544, F.595, I.819 Chain E: G.625 Ligands: PLM.3, POV.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.595, A:I.819 OLC.12: 7 residues within 4Å: Chain D: F.536, Y.544, F.595, I.819 Chain F: G.625 Ligands: PLM.13, POV.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.595, D:I.819 OLC.16: 10 residues within 4Å: Chain D: R.620, I.621 Chain E: L.540, Y.545, F.596, L.603, I.820 Ligands: PLM.17, PLM.20, POV.21 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.596, E:L.603, E:I.820 OLC.23: 10 residues within 4Å: Chain A: R.620, I.621 Chain F: L.540, Y.545, F.596, L.603, I.820 Ligands: PLM.24, PLM.27, POV.28 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.596, F:L.603, F:I.820

14 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.3: 9 residues within 4Å: Chain A: Y.544, W.547, M.548, V.551, Y.554, L.602, F.605 Chain E: F.629 Ligands: OLC.2 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:F.629, A:W.547, A:W.547, A:V.551, A:Y.554, A:L.602, A:F.605 PLM.5: 5 residues within 4Å: Chain B: Y.206 Chain E: M.549, V.552 Ligands: PLM.17, PLM.20 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.552 PLM.6: 5 residues within 4Å: Chain B: V.217, V.220, L.221, N.224 Ligands: PLM.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.217, B:V.220, B:L.221 PLM.8: 5 residues within 4Å: Chain C: Y.206 Chain F: M.549, V.552 Ligands: PLM.24, PLM.27 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.552 PLM.9: 5 residues within 4Å: Chain C: V.217, V.220, L.221, N.224 Ligands: PLM.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.217, C:V.220, C:L.221 PLM.13: 8 residues within 4Å: Chain D: Y.544, W.547, M.548, Y.554, L.602, F.605 Chain F: F.629 Ligands: OLC.12 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:W.547, D:W.547, D:Y.554, D:L.602, D:F.605, F:F.629 PLM.17: 5 residues within 4Å: Ligands: PLM.5, OLC.16, PLM.18, PLM.20, POV.21 No protein-ligand interaction detected (PLIP) PLM.18: 5 residues within 4Å: Chain E: G.594, I.595, F.596 Ligands: PLM.6, PLM.17 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.596, E:F.596 Hydrogen bonds: E:I.595 PLM.19: 5 residues within 4Å: Chain D: C.549 Chain E: L.811, Y.819, I.822, L.825 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.811, E:Y.819, E:I.822, E:L.825 PLM.20: 10 residues within 4Å: Chain E: Y.545, W.548, M.549, V.552, Y.555, F.606 Ligands: PLM.5, OLR.7, OLC.16, PLM.17 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.545, E:Y.545, E:W.548, E:W.548, E:V.552, E:Y.555, E:F.606 PLM.24: 5 residues within 4Å: Ligands: PLM.8, OLC.23, PLM.25, PLM.27, POV.28 No protein-ligand interaction detected (PLIP) PLM.25: 5 residues within 4Å: Chain F: G.594, I.595, F.596 Ligands: PLM.9, PLM.24 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.596, F:F.596 Hydrogen bonds: F:I.595 PLM.26: 5 residues within 4Å: Chain A: C.549 Chain F: L.811, Y.819, I.822, L.825 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.811, F:Y.819, F:I.822, F:L.825 PLM.27: 10 residues within 4Å: Chain F: Y.545, W.548, M.549, V.552, Y.555, F.606 Ligands: PLM.8, OLR.10, OLC.23, PLM.24 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.545, F:Y.545, F:W.548, F:W.548, F:V.552, F:Y.555, F:F.606

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.4: 12 residues within 4Å: Chain A: G.534, V.535, F.536, Y.818, I.819, V.821, G.823, L.826 Chain B: A.117, A.167, I.174 Ligands: OLC.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.536, A:Y.818, A:Y.818, A:I.819, A:V.821, A:L.826, B:A.167 POV.14: 9 residues within 4Å: Chain C: A.117, I.174 Chain D: G.534, V.535, F.536, Y.818, I.819, L.826 Ligands: OLC.12 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.536, D:L.826 POV.21: 5 residues within 4Å: Chain E: V.536, F.537, L.827 Ligands: OLC.16, PLM.17 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.537, E:L.827 Hydrogen bonds: E:V.536 POV.28: 6 residues within 4Å: Chain F: V.536, F.537, Y.819, L.827 Ligands: OLC.23, PLM.24 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:F.537, F:Y.819, F:L.827 Hydrogen bonds: F:V.536

2 x OLR: 6-[(1~{S})-1-[1-[5-(2-hydroxyethyloxy)pyridin-2-yl]pyrazol-3-yl]ethyl]-3~{H}-1,3-benzothiazol-2-one(Non-covalent)

OLR.7: 14 residues within 4Å: Chain B: M.35, W.44, N.172, V.176, Y.199, F.205, Y.206, G.208, G.209 Chain E: Y.545, E.546, M.549, F.553 Ligands: PLM.20 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain B Hydrophobic interactions: E:Y.545, E:E.546, E:F.553, E:F.553, B:V.176, B:F.205, B:Y.206 Hydrogen bonds: B:N.172, B:N.172, B:Y.199, B:Y.206 pi-Stacking: B:Y.201, B:F.205 OLR.10: 14 residues within 4Å: Chain C: M.35, W.44, N.172, V.176, Y.199, F.205, Y.206, G.208, G.209 Chain F: Y.545, E.546, M.549, F.553 Ligands: PLM.27 13 PLIP interactions: 4 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: F:Y.545, F:E.546, F:F.553, F:F.553, C:V.176, C:F.205, C:Y.206 Hydrogen bonds: C:N.172, C:N.172, C:Y.199, C:Y.206 pi-Stacking: C:Y.201, C:F.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Modulatory mechanisms of TARP gamma 8-selective AMPA receptor therapeutics. Nat Commun (2023)

Release Date

2023-04-19

Peptides

Isoform Flip of Glutamate receptor 2: AD
Voltage-dependent calcium channel gamma-8 subunit: BC
Isoform Flip of Glutamate receptor 1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
D

B
I

C
J

E
C

F
A

Membrane

We predict this structure to be a membrane protein.
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Isoform Flip of Glutamate receptor 2

Voltage-dependent calcium channel gamma-8 subunit

Isoform Flip of Glutamate receptor 1

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