SMTL ID : 8ayo.1

Open 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 GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 10 residues within 4Å: Chain A: Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.677, L.726, E.727 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.472 Hydrogen bonds: A:P.500, A:T.502, A:G.675, A:S.676, A:T.677 Salt bridges: A:R.507 GLU.7: 10 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.471 Hydrogen bonds: B:P.499, B:T.501, B:S.675, B:T.676, E.7, E.7 Salt bridges: B:R.506 GLU.10: 10 residues within 4Å: Chain C: Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.677, L.726, E.727 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:Y.472 Hydrogen bonds: C:P.500, C:T.502, C:G.675, C:S.676, C:T.677 Salt bridges: C:R.507 GLU.24: 10 residues within 4Å: Chain F: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726 8 PLIP interactions: 6 interactions with chain F, 2 Ligand-Ligand interactions Hydrophobic interactions: F:Y.471 Hydrogen bonds: F:P.499, F:T.501, F:S.675, F:T.676, E.24, E.24 Salt bridges: F:R.506

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 11 residues within 4Å: Chain A: P.516, F.517, M.518, S.519, L.773, S.776, L.781, D.782, K.785 Chain F: K.751, G.752 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.773 Hydrogen bonds: A:S.776, A:S.776 CYZ.8: 12 residues within 4Å: Chain B: K.514, P.515, F.516, M.517, S.518, L.772, S.775, D.781, K.784 Chain C: S.751, K.752, G.753 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:S.751, B:S.518, B:S.775, B:S.775 Hydrophobic interactions: B:K.514, B:L.772 CYZ.11: 11 residues within 4Å: Chain B: K.751, G.752 Chain C: P.516, F.517, M.518, S.519, L.773, S.776, L.781, D.782, K.785 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.773 Hydrogen bonds: C:S.776, C:S.776 CYZ.25: 12 residues within 4Å: Chain A: S.751, K.752, G.753 Chain F: K.514, P.515, F.516, M.517, S.518, L.772, S.775, D.781, K.784 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:K.514, F:L.772, A:K.752 Hydrogen bonds: F:S.518, F:S.775, F:S.775, A:S.751

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

OLC.3: 8 residues within 4Å: Chain A: F.537, L.540, Y.545, I.820 Chain F: G.624 Ligands: PLM.4, PLM.5, POV.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.540 OLC.9: 5 residues within 4Å: Chain A: I.622, F.629 Chain B: F.536, L.539, F.595 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.536, B:F.595, A:I.622, A:F.629 OLC.12: 8 residues within 4Å: Chain B: G.624 Chain C: F.537, L.540, Y.545, I.820 Ligands: PLM.13, PLM.14, POV.15 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.540 OLC.26: 5 residues within 4Å: Chain C: I.622, F.629 Chain F: F.536, L.539, F.595 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:I.622, C:F.629, F:F.536, F:F.595

10 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 8 residues within 4Å: Chain A: Y.545, W.548, M.549, V.552 Ligands: OLC.3, PLM.5, PLM.20, OIJ.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.545, A:Y.545, A:W.548, A:W.548, A:V.552 PLM.5: 4 residues within 4Å: Chain A: Y.555 Ligands: OLC.3, PLM.4, POV.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.555 PLM.13: 8 residues within 4Å: Chain C: Y.545, W.548, M.549, V.552 Ligands: OLC.12, PLM.14, PLM.16, OIJ.17 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.545, C:Y.545, C:W.548, C:W.548, C:V.552 PLM.14: 4 residues within 4Å: Chain C: Y.555 Ligands: OLC.12, PLM.13, POV.15 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.555 PLM.16: 5 residues within 4Å: Chain C: M.549 Chain D: S.200, Y.206 Ligands: PLM.13, OIJ.17 No protein-ligand interaction detected (PLIP) PLM.18: 3 residues within 4Å: Chain D: A.117 Chain F: G.823 Ligands: PLM.19 No protein-ligand interaction detected (PLIP) PLM.19: 9 residues within 4Å: Chain D: A.117, L.120, L.121, I.174, V.178 Chain F: V.535, Y.818, G.822 Ligands: PLM.18 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:L.120, D:I.174, D:V.178, F:Y.818 Hydrogen bonds: D:L.121 PLM.20: 5 residues within 4Å: Chain A: M.549 Chain E: S.200, Y.206 Ligands: PLM.4, OIJ.23 No protein-ligand interaction detected (PLIP) PLM.21: 3 residues within 4Å: Chain B: G.823 Chain E: A.117 Ligands: PLM.22 No protein-ligand interaction detected (PLIP) PLM.22: 9 residues within 4Å: Chain B: V.535, Y.818, G.822 Chain E: A.117, L.120, L.121, I.174, V.178 Ligands: PLM.21 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:L.120, E:I.174, E:V.178, B:Y.818 Hydrogen bonds: E:L.121

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

POV.6: 8 residues within 4Å: Chain A: I.595, F.596 Chain E: V.217, V.220, L.221, N.224 Ligands: OLC.3, PLM.5 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:V.217, E:V.220, E:L.221, A:F.596 Hydrogen bonds: E:N.224, A:F.596 POV.15: 8 residues within 4Å: Chain C: I.595, F.596 Chain D: V.217, V.220, L.221, N.224 Ligands: OLC.12, PLM.14 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.217, D:V.220, D:L.221, C:F.596 Hydrogen bonds: D:N.224, C:F.596

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.17: 15 residues within 4Å: Chain C: Y.545, E.546, M.549, F.553 Chain D: M.35, N.172, V.176, I.180, F.205, Y.206, G.208, G.209, L.210 Ligands: PLM.13, PLM.16 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Hydrophobic interactions: C:F.553, D:V.176, D:I.180, D:Y.206 Hydrogen bonds: D:N.172, D:N.172, D:Y.206, D:Y.206 pi-Stacking: D:F.205, D:F.205, D:Y.206 OIJ.23: 15 residues within 4Å: Chain A: Y.545, E.546, M.549, F.553 Chain E: M.35, N.172, V.176, I.180, F.205, Y.206, G.208, G.209, L.210 Ligands: PLM.4, PLM.20 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:V.176, E:I.180, E:Y.206, A:F.553 Hydrogen bonds: E:N.172, E:N.172, E:Y.206, E:Y.206 pi-Stacking: E:F.205, E:F.205, E: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 1: AC
Isoform Flip of Glutamate receptor 2: BF
Voltage-dependent calcium channel gamma-8 subunit: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
D

F
B

D
I

E
J

Membrane

We predict this structure to be a membrane protein.
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Isoform Flip of Glutamate receptor 1

Isoform Flip of Glutamate receptor 2

Voltage-dependent calcium channel gamma-8 subunit

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