SMTL ID : 3lsl.1 (1 other biounit)

Piracetam bound to the ligand binding domain of GluA2 (flop form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 12 residues within 4Å: Chain A: Y.58, P.86, L.87, T.88, R.93, L.135, G.138, S.139, T.140, E.190, M.193, Y.217 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.58, A:L.135 Hydrogen bonds: A:P.86, A:T.88, A:S.139, A:T.140, A:T.140, A:E.190, E.1, E.1, E.1 Water bridges: A:L.135, A:G.138 Salt bridges: A:R.93 GLU.7: 12 residues within 4Å: Chain B: Y.58, P.86, L.87, T.88, R.93, L.135, G.138, S.139, T.140, E.190, M.193, Y.217 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.58, B:L.135 Hydrogen bonds: B:P.86, B:T.88, B:T.88, B:T.88, B:S.139, B:T.140, E.7, E.7, E.7 Water bridges: B:T.140, B:K.141 Salt bridges: B:R.93

6 x PZI: 2-(2-oxopyrrolidin-1-yl)acetamide(Non-covalent)

PZI.2: 10 residues within 4Å: Chain A: Y.32, F.103, M.104, N.239, L.244, D.245, K.248 Chain B: S.214 Ligands: PZI.3, PZI.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:K.248 PZI.3: 5 residues within 4Å: Chain A: D.245, N.249 Chain B: D.213, S.214 Ligands: PZI.2 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.214 Hydrogen bonds: A:N.249, A:N.249 PZI.4: 9 residues within 4Å: Chain A: I.89, P.102, S.214, K.215, G.216 Chain B: P.102, S.105, N.239 Ligands: PZI.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.216, A:G.216 PZI.8: 8 residues within 4Å: Chain A: P.102, S.105 Chain B: I.89, P.102, S.214, K.215, G.216 Ligands: PZI.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.216 Water bridges: A:N.239 PZI.9: 9 residues within 4Å: Chain A: S.214 Chain B: Y.32, F.103, M.104, N.239, L.244, D.245, K.248 Ligands: PZI.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.32, B:Y.32, B:K.248 Water bridges: B:N.239, B:L.244 PZI.10: 6 residues within 4Å: Chain A: N.211, L.212, D.213, S.214 Chain B: D.245, N.249 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.245, B:N.249, B:N.249 Water bridges: A:S.214

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 1 residues within 4Å: Chain A: H.20 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.20, H2O.5 ZN.6: 3 residues within 4Å: Chain A: E.39, K.42, H.43 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.43 ZN.11: 1 residues within 4Å: Chain B: H.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.20 ZN.12: 2 residues within 4Å: Chain B: E.39, H.43 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.39, B:H.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmed, A.H. et al., Piracetam Defines a New Binding Site for Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazole-propionic Acid (AMPA) Receptors. J.Med.Chem. (2010)

Release Date

2010-03-16

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Glutamate receptor 2

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