SMTL ID : 9qdn.1

GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

16 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.1: 9 residues within 4Å: Chain A: L.114, N.133, S.137, I.140, F.141 Chain B: L.813, F.816, C.817 Ligands: PLM.3 Ligand excluded by PLIP PLM.2: 10 residues within 4Å: Chain A: F.97, L.98, F.107, I.151, V.155 Chain B: V.516, Y.799, G.806, L.807 Ligands: PLM.7 Ligand excluded by PLIP PLM.3: 6 residues within 4Å: Chain B: G.806, M.809, L.810, L.813, C.817 Ligands: PLM.1 Ligand excluded by PLIP PLM.6: 10 residues within 4Å: Chain B: L.520, Y.525, W.528, I.531, Y.535, L.583, F.586, M.587 Chain F: F.609 Ligands: OLC.4 Ligand excluded by PLIP PLM.7: 9 residues within 4Å: Chain B: V.516, F.517, Y.799, G.803, G.804, L.807 Chain F: V.606 Ligands: PLM.2, OLC.4 Ligand excluded by PLIP PLM.8: 9 residues within 4Å: Chain C: G.806, M.809, L.810, L.813, C.817 Chain E: S.144, L.147, S.148 Ligands: PLM.12 Ligand excluded by PLIP PLM.11: 9 residues within 4Å: Chain B: F.609 Chain C: L.520, Y.525, W.528, I.531, Y.535, L.583, F.586 Ligands: OLC.9 Ligand excluded by PLIP PLM.12: 7 residues within 4Å: Chain C: C.817 Chain E: L.114, N.133, S.137, I.140, F.141 Ligands: PLM.8 Ligand excluded by PLIP PLM.13: 10 residues within 4Å: Chain D: L.110, S.144, L.147, S.148 Chain F: G.806, M.809, L.810, L.813, C.817 Ligands: PLM.14 Ligand excluded by PLIP PLM.14: 10 residues within 4Å: Chain D: L.114, N.133, S.137, I.140, F.141, S.144 Chain F: L.813, F.816, C.817 Ligands: PLM.13 Ligand excluded by PLIP PLM.17: 8 residues within 4Å: Chain F: L.520, Y.525, W.528, I.531, Y.535, L.583, F.586 Ligands: OLC.15 Ligand excluded by PLIP PLM.18: 9 residues within 4Å: Chain G: G.806, M.809, L.810, L.813, C.817 Chain H: I.140, S.144, L.147 Ligands: PLM.24 Ligand excluded by PLIP PLM.21: 7 residues within 4Å: Chain C: F.609 Chain G: L.520, Y.525, W.528, Y.535, F.586 Ligands: OLC.19 Ligand excluded by PLIP PLM.22: 8 residues within 4Å: Chain G: V.516, F.517, Y.799, I.800, G.803, L.807 Ligands: OLC.19, PLM.23 Ligand excluded by PLIP PLM.23: 9 residues within 4Å: Chain G: V.516, Y.799, G.803, G.806 Chain H: F.97, L.98, F.107, V.155 Ligands: PLM.22 Ligand excluded by PLIP PLM.24: 12 residues within 4Å: Chain G: F.816, C.817, S.820, R.821 Chain H: L.114, N.133, L.136, S.137, I.140, F.141, S.144 Ligands: PLM.18 Ligand excluded by PLIP

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

OLC.4: 10 residues within 4Å: Chain B: F.517, L.579, W.580, L.583, I.800 Chain F: R.601, G.605, F.609 Ligands: PLM.6, PLM.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:F.517, B:L.579, B:W.580, B:W.580, B:L.583, B:I.800, F:F.609 OLC.9: 12 residues within 4Å: Chain B: R.601, I.602, G.605, F.609 Chain C: F.517, Y.535, F.576, L.579, L.583, M.587, I.800 Ligands: PLM.11 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.576, C:L.579, C:L.583, C:I.800, C:I.800, B:R.601, B:F.609, B:F.609 OLC.15: 10 residues within 4Å: Chain F: F.517, L.520, F.576, L.579, W.580, L.583, I.800 Chain G: G.605, F.609 Ligands: PLM.17 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:L.520, F:F.576, F:L.579, F:W.580, F:I.800, F:I.800, G:F.609, G:F.609, G:F.609 OLC.19: 10 residues within 4Å: Chain C: L.598, R.601, G.605, F.609 Chain G: F.517, L.520, L.583, I.800 Ligands: PLM.21, PLM.22 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:L.598, C:R.601, C:F.609, C:F.609, G:F.517, G:L.520, G:L.583, G:I.800

4 x E2Q: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide(Non-covalent)

E2Q.5: 11 residues within 4Å: Chain B: E.404, Y.407, Y.452, P.480, L.481, T.482, R.487, T.688, E.707, M.710, Y.734 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.734 Hydrogen bonds: B:P.480, B:T.482, B:T.482, B:R.487, B:R.487, B:T.688, B:T.688, B:E.707 pi-Stacking: B:Y.452, B:Y.452 E2Q.10: 11 residues within 4Å: Chain C: E.404, Y.407, Y.452, P.480, L.481, T.482, R.487, T.688, E.707, M.710, Y.734 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.404, C:P.480, C:T.482, C:T.482, C:R.487, C:R.487 pi-Stacking: C:Y.452, C:Y.452 E2Q.16: 11 residues within 4Å: Chain F: E.404, Y.407, Y.452, P.480, L.481, T.482, R.487, T.688, E.707, M.710, Y.734 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.404, F:P.480, F:T.482, F:T.482, F:R.487, F:R.487 pi-Stacking: F:Y.452, F:Y.452 E2Q.20: 9 residues within 4Å: Chain G: Y.452, P.480, L.481, T.482, R.487, T.688, E.707, M.710, Y.734 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:Y.734 Hydrogen bonds: G:P.480, G:T.482, G:T.482, G:R.487, G:R.487, G:T.688, G:T.688, G:E.707 pi-Stacking: G:Y.452, G:Y.452

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vega-Gutierrez, C. et al., GluA4 AMPA receptor gating mechanisms and modulation by auxiliary subunits. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-09-24

Peptides

Voltage-dependent calcium channel gamma-2 subunit: ADEH
Isoform 2 of Glutamate receptor 4: BCFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
G

E
E

H
F

B
D

C
A

F
C

G
B

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent calcium channel gamma-2 subunit

Isoform 2 of Glutamate receptor 4

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