SMTL ID : 8fpl.1

LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100uM CNQX (Closed-CaNaMg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x Y4Y: 6-(aminomethyl)-7-nitro-1,4-dihydroquinoxaline-2,3-dione(Non-covalent)

Y4Y.1: 9 residues within 4Å: Chain A: E.423, Y.471, P.499, L.500, T.501, R.506, E.726, M.729, Y.753 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:Y.753, A:Y.753 pi-Stacking: A:Y.471, A:Y.471 Y4Y.3: 9 residues within 4Å: Chain B: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, E.726, Y.753 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.471, B:Y.471 Hydrogen bonds: B:Y.471, B:P.499, B:T.501, B:R.506, B:R.506 pi-Stacking: B:Y.471 Y4Y.5: 9 residues within 4Å: Chain C: E.423, Y.471, P.499, L.500, T.501, R.506, E.726, M.729, Y.753 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.471, C:Y.471 Hydrogen bonds: C:P.499, C:T.501, C:R.506, C:R.506, C:Y.753, C:Y.753 pi-Stacking: C:Y.471 Y4Y.7: 9 residues within 4Å: Chain D: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, E.726, Y.753 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.471, D:Y.471 Hydrogen bonds: D:Y.471, D:P.499, D:T.501, D:R.506, D:R.506 pi-Stacking: D:Y.471

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 15 residues within 4Å: Chain A: K.514, P.515, F.516, M.517, S.518, L.772, S.775, L.780, D.781, K.784 Chain B: I.502, P.515, S.750, K.751, G.752 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:K.514, A:P.515, A:L.772, B:I.502, B:I.502, B:P.515 Hydrogen bonds: A:S.518, A:S.518, A:S.775, A:S.775, B:S.750, B:S.750 CYZ.4: 14 residues within 4Å: Chain A: I.502, S.750, K.751, G.752 Chain B: K.514, P.515, F.516, M.517, S.518, L.772, S.775, L.780, D.781, K.784 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.514, B:P.515, B:L.772, A:I.502, A:I.502 Hydrogen bonds: B:S.518, B:S.518, B:S.775, B:S.775, A:S.750, A:S.750 CYZ.6: 14 residues within 4Å: Chain C: K.514, P.515, F.516, M.517, S.518, L.772, S.775, L.780, D.781, K.784 Chain D: I.502, S.750, K.751, G.752 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:K.514, C:P.515, C:L.772, D:I.502, D:I.502 Hydrogen bonds: C:S.518, C:S.518, C:S.775, C:S.775, D:S.750, D:S.750 CYZ.8: 14 residues within 4Å: Chain C: I.502, P.515, S.750, K.751, G.752 Chain D: K.514, P.515, F.516, M.517, S.518, L.772, S.775, L.780, D.781 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.502, C:I.502, C:P.515, D:K.514, D:P.515, D:L.772 Hydrogen bonds: C:S.750, D:F.516, D:S.775, D:S.775

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakagawa, T. et al., The open gate of the AMPA receptor forms a Ca 2+ binding site critical in regulating ion transport. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-28

Peptides

Glutamate receptor 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
D

Glutamate receptor 2

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