SMTL ID : 8fpc.1

Conformation 1 of the ligand binding domain (LBDconf1) 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 100mM glutamate (Open-CaNaMg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726, Y.753 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Y.471, A:L.671, A:E.726 Hydrogen bonds: A:P.499, A:T.501, A:S.675, A:S.675, A:S.675, A:T.676, A:T.676, A:E.726 Water bridges: A:T.707 Salt bridges: A:R.506 GLU.3: 10 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, E.726, Y.753 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.471, B:E.726 Hydrogen bonds: B:P.499, B:T.501, B:T.501, B:S.675, B:T.676, B:T.676, B:E.726, B:E.726, E.3 Water bridges: B:L.671 Salt bridges: B:R.506 GLU.5: 11 residues within 4Å: Chain C: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726, Y.753 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:Y.471, C:E.726 Hydrogen bonds: C:T.501, C:T.501, C:S.675, C:S.675, C:S.675, C:T.676, C:T.676, C:E.726 Water bridges: C:T.707 Salt bridges: C:R.506 GLU.7: 10 residues within 4Å: Chain D: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, E.726, Y.753 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.471 Hydrogen bonds: D:P.499, D:T.501, D:T.501, D:S.675, D:T.676, D:T.676, D:E.726, D:E.726, E.7 Water bridges: D:L.671 Salt bridges: D:R.506

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

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
A

B
B

C
C

D
D

Glutamate receptor 2

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