SMTL ID : 8fq2.1

LBD conformation 1 (LBDconf1) 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: 12 residues within 4Å: Chain A: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, L.725, E.726, M.729 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.471, A:L.671 Hydrogen bonds: A:T.501, A:G.674, A:T.676, A:T.676, E.1, E.1 Salt bridges: A:R.506 GLU.3: 12 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, L.725, E.726, Y.753 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.471, B:L.671 Hydrogen bonds: B:P.499, B:T.501, B:T.501, B:S.675, B:T.676, B:T.676, B:E.726, E.3 Salt bridges: B:R.506 GLU.5: 12 residues within 4Å: Chain C: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, L.725, E.726, Y.753 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.471, C:L.671 Hydrogen bonds: C:P.499, C:T.501, C:T.501, C:S.675, C:T.676, C:T.676, C:E.726, E.5 Salt bridges: C:R.506 GLU.7: 12 residues within 4Å: Chain D: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, L.725, E.726, M.729 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.471, D:L.671 Hydrogen bonds: D:T.501, D:G.674, D:T.676, D:T.676, E.7, E.7 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 B: I.502, P.515, S.750, K.751, G.752 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:K.514, A:L.772, B:I.502, B:I.502, B:P.515, B:K.751 Hydrogen bonds: A:S.518, A:S.775, A:S.775, B:S.750, B:S.750 CYZ.4: 13 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 9 PLIP interactions: 5 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.775, B:S.775, A:S.750, A:S.750 CYZ.6: 13 residues within 4Å: Chain C: K.514, P.515, F.516, M.517, S.518, L.772, S.775, L.780, D.781 Chain D: I.502, S.750, K.751, G.752 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:K.514, C:L.772, D:I.502, D:I.502 Hydrogen bonds: C:S.518, C:S.775, C:S.775, D:S.750, D:S.750 CYZ.8: 15 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, K.784 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:K.514, D:L.772, C:I.502, C:I.502, C:P.515 Hydrogen bonds: 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
A

B
D

C
B

D
C

Glutamate receptor 2

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