SMTL ID : 8ayl.1

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059

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: 15 residues within 4Å: Chain A: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.707, L.725, E.726, M.729, Y.753 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:S.675, A:S.675, A:S.675, A:S.675 pi-Stacking: A:Y.471 Halogen bonds: A:Y.753 ZK1.10: 17 residues within 4Å: Chain D: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, L.672, G.675, S.676, T.677, T.708, L.726, E.727, T.729, M.730, Y.754 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:P.500, D:T.502, D:R.507, D:S.676, D:S.676, D:S.676, D:S.676 pi-Stacking: D:Y.472 Halogen bonds: D:Y.754 ZK1.15: 15 residues within 4Å: Chain E: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.707, L.725, E.726, M.729, Y.753 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:P.499, E:T.501, E:R.506, E:R.506, E:S.675, E:S.675, E:S.675, E:S.675 pi-Stacking: E:Y.471 Halogen bonds: E:Y.753 ZK1.20: 17 residues within 4Å: Chain F: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, L.672, G.675, S.676, T.677, T.708, L.726, E.727, T.729, M.730, Y.754 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:P.500, F:T.502, F:R.507, F:S.676, 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: 17 residues within 4Å: Chain A: F.536, L.539, Y.544, Y.554, F.595, L.598, W.599, L.602, I.819 Chain F: L.618, R.621, I.622, G.625, V.626, F.629 Ligands: PLM.3, POV.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.595, A:L.602, A:I.819 OLC.11: 20 residues within 4Å: Chain A: L.617, R.620, I.621, G.624, V.625, F.628 Chain D: F.537, L.540, Y.545, Y.555, F.596, L.599, W.600, L.603, M.607, I.820 Ligands: POV.6, PLM.12, PLM.13, POV.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.625, D:F.596, D:I.820 OLC.16: 17 residues within 4Å: Chain D: L.618, R.621, I.622, G.625, V.626, F.629 Chain E: F.536, L.539, Y.544, Y.554, F.595, L.598, W.599, L.602, I.819 Ligands: PLM.17, POV.18 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.595, E:L.602, E:I.819 OLC.21: 20 residues within 4Å: Chain E: L.617, R.620, I.621, G.624, V.625, F.628 Chain F: F.537, L.540, Y.545, Y.555, F.596, L.599, W.600, L.603, M.607, I.820 Ligands: POV.8, PLM.22, PLM.23, POV.24 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:V.625, F:F.596, F:I.820

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

PLM.3: 12 residues within 4Å: Chain A: L.539, Y.544, W.547, M.548, I.550, V.551, Y.554, L.602, F.605, M.606 Chain F: F.629 Ligands: OLC.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:Y.544, A:F.605, F:F.629 PLM.9: 10 residues within 4Å: Chain B: Y.206, I.213 Chain D: M.549, V.552, F.553, I.556 Ligands: OIJ.5, POV.6, PLM.12, PLM.13 No protein-ligand interaction detected (PLIP) PLM.12: 15 residues within 4Å: Chain A: F.628 Chain D: L.540, Y.545, W.548, M.549, I.551, V.552, Y.555, L.603, F.606, M.607 Ligands: OIJ.5, PLM.9, OLC.11, PLM.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.545, D:Y.545, D:Y.545, D:W.548, A:F.628 PLM.13: 9 residues within 4Å: Chain D: M.549, V.552, Y.555, L.603 Ligands: POV.6, PLM.9, OLC.11, PLM.12, POV.14 No protein-ligand interaction detected (PLIP) PLM.17: 12 residues within 4Å: Chain D: F.629 Chain E: L.539, Y.544, W.547, M.548, I.550, V.551, Y.554, L.602, F.605, M.606 Ligands: OLC.16 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:Y.544, E:F.605, D:F.629 PLM.19: 10 residues within 4Å: Chain C: Y.206, I.213 Chain F: M.549, V.552, F.553, I.556 Ligands: OIJ.7, POV.8, PLM.22, PLM.23 No protein-ligand interaction detected (PLIP) PLM.22: 15 residues within 4Å: Chain E: F.628 Chain F: L.540, Y.545, W.548, M.549, I.551, V.552, Y.555, L.603, F.606, M.607 Ligands: OIJ.7, PLM.19, OLC.21, PLM.23 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:F.628, F:Y.545, F:Y.545, F:Y.545, F:W.548 PLM.23: 9 residues within 4Å: Chain F: M.549, V.552, Y.555, L.603 Ligands: POV.8, PLM.19, OLC.21, PLM.22, POV.24 No protein-ligand interaction detected (PLIP)

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

POV.4: 19 residues within 4Å: Chain A: G.534, V.535, F.536, Y.818, I.819, V.821, G.822, G.823, L.826 Chain C: A.117, L.120, L.121, V.124, F.130, I.174, V.178 Chain F: I.622, V.626 Ligands: OLC.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.818, A:L.826 POV.6: 16 residues within 4Å: Chain A: L.617 Chain B: I.213, V.217, V.220, L.221, N.224 Chain D: Y.555, I.556, V.560, G.594, I.595, F.596, L.599 Ligands: PLM.9, OLC.11, PLM.13 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:I.595, B:I.213, B:V.220 Hydrogen bonds: D:I.595, D:F.596, B:N.224 POV.8: 16 residues within 4Å: Chain C: I.213, V.217, V.220, L.221, N.224 Chain E: L.617 Chain F: Y.555, I.556, V.560, G.594, I.595, F.596, L.599 Ligands: PLM.19, OLC.21, PLM.23 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:I.213, C:V.220, F:I.595 Hydrogen bonds: C:N.224, F:I.595, F:F.596 POV.14: 12 residues within 4Å: Chain A: I.621, V.625 Chain D: G.535, V.536, F.537, Y.819, I.820, G.823, G.824, L.827 Ligands: OLC.11, PLM.13 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.625, D:Y.819 Hydrogen bonds: D:V.536, D:V.536 POV.18: 19 residues within 4Å: Chain B: A.117, L.120, L.121, V.124, F.130, I.174, V.178 Chain D: I.622, V.626 Chain E: G.534, V.535, F.536, Y.818, I.819, V.821, G.822, G.823, L.826 Ligands: OLC.16 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.818, E:L.826 POV.24: 12 residues within 4Å: Chain E: I.621, V.625 Chain F: G.535, V.536, F.537, Y.819, I.820, G.823, G.824, L.827 Ligands: OLC.21, PLM.23 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Y.819, E:V.625 Hydrogen bonds: F:V.536, F:V.536

2 x OIJ: 5-[2-(4-fluorophenyl)-7-(4-oxidanylpiperidin-1-yl)pyrazolo[1,5-c]pyrimidin-3-yl]-1,3-dihydroindol-2-one(Non-covalent)

OIJ.5: 17 residues within 4Å: Chain B: M.35, W.44, N.172, V.176, I.180, Y.201, F.205, Y.206, G.208, G.209, L.210 Chain D: Y.545, E.546, M.549, F.553 Ligands: PLM.9, PLM.12 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:V.176, B:I.180, B:F.205, B:F.205, D:Y.545, D:F.553, D:F.553 Hydrogen bonds: B:N.172, B:N.172 pi-Stacking: B:F.205, B:F.205, B:Y.206 OIJ.7: 17 residues within 4Å: Chain C: M.35, W.44, N.172, V.176, I.180, Y.201, F.205, Y.206, G.208, G.209, L.210 Chain F: Y.545, E.546, M.549, F.553 Ligands: PLM.19, PLM.22 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: F:Y.545, F:F.553, F:F.553, C:V.176, C:I.180, C:F.205, C:F.205 Hydrogen bonds: C:N.172, C:N.172 pi-Stacking: C:F.205, C:F.205, C:Y.206

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: AE
Voltage-dependent calcium channel gamma-8 subunit: BC
Isoform Flip of Glutamate receptor 1: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
D

B
J

C
I

D
A

F
C

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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