SMTL ID : 7f3o.2 (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

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain A: E.166 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.166, A:E.166, H2O.9 ZN.3: 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: 4 residues within 4Å: Chain B: K.20, H.23, E.30 Ligands: ACT.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, B:E.30, B:E.30, ACT.11 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.13: 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.20

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 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, A:E.193, E.2, E.2, E.2 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:S.142, B:T.143, B:T.143, B:E.193, E.7, E.7, E.7 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

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

ACT.4: 4 residues within 4Å: Chain A: A.134, R.180, K.187, Y.188 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.134, A:Y.188 Water bridges: A:R.180 Salt bridges: A:R.180 ACT.10: 4 residues within 4Å: Chain B: A.134, R.180, K.187, Y.188 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.134, B:Y.188 Water bridges: B:R.180 Salt bridges: B:R.180 ACT.11: 4 residues within 4Å: Chain B: K.20, H.23, E.30 Ligands: ZN.8 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.20, B:H.23

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:N.214, A:S.217 GOL.12: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.214, B:D.216 Water bridges: B:S.217

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.6: 20 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, N.242, L.247 Chain B: K.104, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, N.242 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.105, A:L.247, B:P.105 Hydrogen bonds: A:G.219 Water bridges: A:K.218, B:K.218

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
C

B
D

Glutamate receptor 2

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