SMTL ID : 5ybg.2 (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: 3 Ligand-Ligand interactions, 11 interactions with chain A Hydrogen bonds: E.1, E.1, E.1, A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, A:E.193 Hydrophobic interactions: A:Y.61, A:L.138 Water bridges: A:L.138 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:T.91, B:S.142, B:T.143, B:T.143, 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: K.104, P.105, F.106, M.107, S.108, S.217, K.218, V.238, L.239, N.242 Chain B: P.105, F.106, M.107, S.108, S.217, K.218, G.219, V.238, N.242, L.247 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.105, A:P.105, A:V.238, A:L.239, B:P.105, B:P.105, B:K.218 Hydrogen bonds: A:P.105 Water bridges: B:G.219, B:G.219

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.23, E.30 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.23, A:E.30, A:E.30, H2O.9 ZN.4: 4 residues within 4Å: Chain A: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:H.46, H2O.9 ZN.8: 3 residues within 4Å: Chain B: K.20, H.23, E.30 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.23, B:E.30, B:E.30 ZN.9: 4 residues within 4Å: Chain B: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.20 ZN.11: 1 residues within 4Å: Chain B: E.166 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.166, B:E.166, H2O.21

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

ACT.5: 4 residues within 4Å: Chain A: A.134, R.180, K.187, Y.188 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.188 Water bridges: A:R.180, A:R.180, A:K.183 Salt bridges: A:R.180 ACT.6: 10 residues within 4Å: Chain A: F.102, S.103, K.104, R.231, N.235 Chain B: F.102, S.103, K.104, R.231, N.235 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.235 Water bridges: B:R.231, A:R.231 Salt bridges: B:K.104, A:K.104 ACT.10: 3 residues within 4Å: Chain B: R.180, K.187, Y.188 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.188 Water bridges: B:R.180, B:R.180 Salt bridges: B:R.180

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
C

B
D

Glutamate receptor 2,Glutamate receptor 2

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