SMTL ID : 8fq3.1

LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform N619K mutant 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/N619K)

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, S.675, T.676, L.725, E.726, Y.753 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.471, A:L.671, A:E.726 Hydrogen bonds: A:P.499, A:T.501, A:T.501, A:S.675, A:T.676, A:E.726, A:E.726, E.1 Salt bridges: A:R.506 GLU.3: 10 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, L.671, G.674, S.675, T.676, E.726, Y.753 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:Y.471, B:L.671, B:E.726 Hydrogen bonds: B:P.499, B:T.501, B:G.674, B:S.675, B:T.676, B:T.676, B:E.726 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, S.675, T.676, L.725, E.726, Y.753 13 PLIP interactions: 1 Ligand-Ligand interactions, 12 interactions with chain C Hydrogen bonds: E.5, C:P.499, C:T.501, C:T.501, C:S.675, C:S.675, C:T.676, C:E.726, C:E.726 Hydrophobic interactions: C:Y.471, C:L.671, C:E.726 Salt bridges: C:R.506 GLU.7: 10 residues within 4Å: Chain D: Y.471, P.499, L.500, T.501, L.671, G.674, S.675, T.676, E.726, Y.753 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:Y.471, D:L.671, D:E.726 Hydrogen bonds: D:P.499, D:T.501, D:G.674, D:S.675, D:T.676, D:T.676, D:E.726 Salt bridges: D:R.506

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 13 residues within 4Å: Chain A: K.514, P.515, M.517, S.518, L.772, S.775, L.780, D.781, K.784 Chain B: I.502, S.750, K.751, G.752 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.514, A:L.772, B:I.502, B:I.502 Hydrogen bonds: A:S.518, A:S.775, A:S.775, 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 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.514, 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 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.502, D:I.502, C:K.514, C:L.772 Hydrogen bonds: D:S.750, C:S.775, C:S.775 CYZ.8: 14 residues within 4Å: Chain C: I.502, 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: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:K.514, D:L.772, C:I.502, C:I.502 Hydrogen bonds: D:S.518, D:S.518, D:S.775, D:S.775, C:S.750, C: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
B

B
C

C
D

D
A

Glutamate receptor 2

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