SMTL ID : 5ybg.1 (2 other biounits)

Crystal structure of the GluA2o LBD in complex with glutamate and LY451395

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.1, E.1, E.1 Water bridges: A:K.144, A:E.193 Salt bridges: A:R.96 GLU.7: 11 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, B:E.193, E.7, E.7, E.7 Water bridges: B:L.138 Salt bridges: B:R.96

1 x 8SO: N-[(2R)-2-[4-[4-[2-(methylsulfonylamino)ethyl]phenyl]phenyl]propyl]propane-2-sulfonamide(Non-covalent)

8SO.2: 20 residues within 4Å: Chain A: I.92, K.104, P.105, M.107, S.108, S.217, K.218, G.219, L.239, N.242 Chain B: K.104, P.105, M.107, S.108, S.217, K.218, G.219, L.239, N.242 Ligands: GOL.5 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.105, A:P.105, A:K.218, B:P.105, B:P.105, B:N.242 Hydrogen bonds: A:P.105, B:P.105

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.23 Ligands: ACT.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.23, H2O.1 ZN.6: 3 residues within 4Å: Chain A: E.42, H.46, L.241 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:H.46 ZN.8: 5 residues within 4Å: Chain B: E.42, K.45, H.46, L.241, Q.244 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.6, H2O.13

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: M.19, K.20, K.21, H.23 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.23

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: F.106, M.107, S.108, L.247, D.248, K.251 Chain B: S.217 Ligands: 8SO.2 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.217, A:F.106, A:S.108, A:S.108, A:D.248 Water bridges: A:S.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunugi, A. et al., HBT1, a Novel AMPA Receptor Potentiator with Lower Agonistic Effect, Avoided Bell-Shaped Response in In Vitro BDNF Production. J. Pharmacol. Exp. Ther. (2018)

Release Date

2018-01-17

Peptides

Glutamate receptor 2,Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2,Glutamate receptor 2

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