SMTL ID : 7f3o.3 (2 other biounits)

Crystal structure of the GluA2o LBD in complex with glutamate and TAK-653

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 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 13 PLIP interactions: 10 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:T.91, A:S.142, A:T.143, A:T.143, E.1, E.1, E.1 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.4: 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.4, E.4, E.4 Water bridges: B:L.138 Salt bridges: B:R.96

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.23, E.24 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.23 ZN.5: 4 residues within 4Å: Chain B: E.42, H.46, L.241, Q.244 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.14 ZN.6: 1 residues within 4Å: Chain B: D.65 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.65, B:D.65 ZN.7: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ACT.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, ACT.8

1 x 0YK: 7-(4-cyclohexyloxyphenyl)-9-methyl-4$l^{6}-thia-1$l^{4},5,8-triazabicyclo[4.4.0]deca-1(10),6,8-triene 4,4-dioxide(Non-covalent)

0YK.3: 18 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, N.242 Chain B: K.104, P.105, F.106, M.107, S.217, K.218, G.219, L.239, N.242 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.105, A:P.105 Water bridges: B:K.218, B:G.219, A:K.218 Hydrogen bonds: A:G.219

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

ACT.8: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.24 Salt bridges: B:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, A. et al., Strictly regulated agonist-dependent activation of AMPA-R is the key characteristic of TAK-653 for robust synaptic responses and cognitive improvement. Sci Rep (2021)

Release Date

2021-07-28

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Glutamate receptor 2

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