SMTL ID : 9j8k.1

Crystal structure of the GluA2 ligand binding core (S1S2J) in complex with fluorophore-ligand conjugate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x 01: 2-(3-azanyl-6-azanylidene-4,5-disulfo-xanthen-9-yl)-5-[[1-[4-(2-hydroxy-2-oxoethyl)-2,3-bis(oxidanylidene)-7-(trifluoromethyl)-1~{H}-quinoxalin-6-yl]pyrrol-3-yl]methylcarbamoyl]benzoic acid

01.1: 18 residues within 4Å: Chain A: E.22, Y.25, Y.70, P.98, L.99, T.100, R.105, L.147, S.149, G.150, S.151, R.181, T.182, T.183, E.202, T.204, M.205, Y.229 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.70, A:Y.70, A:L.147, A:T.182, A:Y.229 Hydrogen bonds: A:P.98, A:T.100, A:R.105, A:R.105, A:S.151, A:T.183, A:T.183, A:E.202 Water bridges: A:E.22, A:E.22, A:S.149, A:R.181, A:R.181, A:A.184 Salt bridges: A:R.181 pi-Stacking: A:Y.70

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.40, K.61, T.63 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.40, A:R.40 Salt bridges: A:R.40, A:K.61 SO4.3: 2 residues within 4Å: Chain A: R.73, K.78 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.73 Salt bridges: A:R.73, A:K.78

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: K.29, K.30, N.31, L.35, E.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.30, A:N.31 Water bridges: A:K.29, A:E.42 PEG.5: 4 residues within 4Å: Chain A: R.157, W.168, T.169, R.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.157, A:W.168 Water bridges: A:T.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soga, K. et al., Rapid and reversible fluorescent probe enables repeated snapshot imaging of AMPA receptors during synaptic plasticity. Sci Adv (2025)

Release Date

2025-07-02

Peptides

GluA2 ligand binding core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GluA2 ligand binding core