SMTL ID : 8aym.1

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x XVD: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol(Non-covalent)

XVD.1: 14 residues within 4Å: Chain A: M.35, W.44, N.172, V.176, I.180, F.205, G.208, G.209 Chain B: Y.545, E.546, M.549, C.550, F.553 Ligands: PLM.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.205, B:M.549, B:F.553 Hydrogen bonds: A:N.172, A:N.172, A:F.205 XVD.28: 14 residues within 4Å: Chain E: Y.545, E.546, M.549, C.550, F.553 Chain F: M.35, W.44, N.172, V.176, I.180, F.205, G.208, G.209 Ligands: PLM.25 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.205, E:M.549, E:F.553 Hydrogen bonds: F:N.172, F:N.172, F:F.205

14 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 2 residues within 4Å: Chain A: N.224 Ligands: PLM.5 No protein-ligand interaction detected (PLIP) PLM.5: 3 residues within 4Å: Chain B: I.595, L.599 Ligands: PLM.2 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.595, B:L.599 Salt bridges: B:R.567 PLM.6: 6 residues within 4Å: Chain B: L.811, S.812, Y.819, I.822, L.825 Chain C: A.553 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.811, B:Y.819, B:I.822, B:I.822, B:L.825 Hydrogen bonds: B:S.812 PLM.8: 5 residues within 4Å: Chain A: Y.206 Chain B: Y.545, M.549 Ligands: XVD.1, PLM.9 No protein-ligand interaction detected (PLIP) PLM.9: 4 residues within 4Å: Chain B: M.549, Y.555 Ligands: POV.7, PLM.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.555 PLM.12: 8 residues within 4Å: Chain C: Y.544, W.547, I.550, Y.554, L.602, F.605 Ligands: OLC.11, PLM.13 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.544, C:W.547, C:W.547, C:I.550, C:Y.554, C:L.602, C:F.605 Hydrogen bonds: C:Y.544 PLM.13: 3 residues within 4Å: Chain C: Y.554 Ligands: OLC.11, PLM.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.554 PLM.17: 8 residues within 4Å: Chain D: Y.544, W.547, I.550, Y.554, L.602, F.605 Ligands: OLC.16, PLM.18 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.544, D:W.547, D:W.547, D:I.550, D:Y.554, D:L.602, D:F.605 Hydrogen bonds: D:Y.544 PLM.18: 3 residues within 4Å: Chain D: Y.554 Ligands: OLC.16, PLM.17 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.554 PLM.22: 3 residues within 4Å: Chain E: I.595, L.599 Ligands: PLM.27 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.595, E:L.599 Salt bridges: E:R.567 PLM.23: 6 residues within 4Å: Chain D: A.553 Chain E: L.811, S.812, Y.819, I.822, L.825 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.811, E:Y.819, E:I.822, E:I.822, E:L.825 Hydrogen bonds: E:S.812 PLM.25: 5 residues within 4Å: Chain E: Y.545, M.549 Chain F: Y.206 Ligands: PLM.26, XVD.28 No protein-ligand interaction detected (PLIP) PLM.26: 4 residues within 4Å: Chain E: M.549, Y.555 Ligands: POV.24, PLM.25 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.555 PLM.27: 2 residues within 4Å: Chain F: N.224 Ligands: PLM.22 No protein-ligand interaction detected (PLIP)

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

ZK1.3: 14 residues within 4Å: Chain B: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.708, L.726, E.727, M.730, Y.754 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:P.500, B:T.502, B:R.507, B:S.676, B:S.676, B:S.676, B:E.727 pi-Stacking: B:Y.472, B:Y.472 Halogen bonds: B:Y.754 ZK1.10: 14 residues within 4Å: Chain C: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, E.726, T.728, M.729, Y.753 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:P.499, C:T.501, C:R.506, C:R.506, C:S.675, C:S.675, C:S.675 pi-Stacking: C:Y.471 Halogen bonds: C:Y.753 ZK1.15: 14 residues within 4Å: Chain D: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, E.726, T.728, M.729, Y.753 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:P.499, D:T.501, D:R.506, D:R.506, D:S.675, D:S.675, D:S.675 pi-Stacking: D:Y.471 Halogen bonds: D:Y.753 ZK1.20: 14 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, L.726, E.727, M.730, Y.754 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:P.500, E:T.502, E:R.507, E:S.676, E:S.676, E:S.676, E:E.727 pi-Stacking: E:Y.472, E:Y.472 Halogen bonds: E:Y.754

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

POV.4: 7 residues within 4Å: Chain B: V.536, F.537, Y.819, I.820, G.823, G.824, L.827 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.819, B:L.827 POV.7: 14 residues within 4Å: Chain A: Y.199, S.200 Chain B: F.537, L.540, Y.545, E.546, W.548, Y.555, L.603, F.606, I.820 Chain C: G.624, F.628 Ligands: PLM.9 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.537, B:Y.545, B:Y.545, B:W.548, B:W.548, B:Y.555, B:L.603, B:F.606, B:I.820, C:F.628 Salt bridges: B:E.546 POV.14: 9 residues within 4Å: Chain C: V.535, F.536, Y.818, I.819 Chain F: A.117, L.120, V.124, V.178 Ligands: OLC.11 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.536 POV.19: 11 residues within 4Å: Chain A: A.117, L.120, V.124, F.130, V.178 Chain D: V.535, F.536, Y.818, I.819, G.823 Ligands: OLC.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.536, A:F.130 POV.21: 7 residues within 4Å: Chain E: V.536, F.537, Y.819, I.820, G.823, G.824, L.827 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.819, E:L.827 POV.24: 14 residues within 4Å: Chain D: G.624, F.628 Chain E: F.537, L.540, Y.545, E.546, W.548, Y.555, L.603, F.606, I.820 Chain F: Y.199, S.200 Ligands: PLM.26 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.537, E:Y.545, E:Y.545, E:W.548, E:W.548, E:Y.555, E:L.603, E:F.606, E:I.820, D:F.628 Salt bridges: E:E.546

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

OLC.11: 11 residues within 4Å: Chain C: F.536, Y.544, F.595, L.598, W.599 Chain E: I.622, G.625, V.626 Ligands: PLM.12, PLM.13, POV.14 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:F.595, C:L.598, C:W.599, E:I.622 Hydrogen bonds: C:Y.544, C:Y.544 OLC.16: 11 residues within 4Å: Chain B: I.622, G.625, V.626 Chain D: F.536, Y.544, F.595, L.598, W.599 Ligands: PLM.17, PLM.18, POV.19 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.595, D:L.598, D:W.599, B:I.622 Hydrogen bonds: D:Y.544, D:Y.544

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

Voltage-dependent calcium channel gamma-8 subunit: AF
Isoform Flip of Glutamate receptor 1: BE
Isoform Flip of Glutamate receptor 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

F
J

B
C

E
A

C
D

D
B

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent calcium channel gamma-8 subunit

Isoform Flip of Glutamate receptor 1

Isoform Flip of Glutamate receptor 2

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