SMTL ID : 6ruq.1

Structure of GluA2cryst in complex the antagonist ZK200775 and the negative allosteric modulator GYKI53655 at 4.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.65 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: Q.328, N.335, K.337, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain C: Q.328, N.335, N.346 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.335

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.2: 7 residues within 4Å: Chain B: K.337, Q.340, N.341, I.345, N.346, S.366, V.368 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.341

4 x GYK: (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide(Non-covalent)

GYK.4: 10 residues within 4Å: Chain A: P.503, S.507, F.508, D.510, P.511, Y.607, L.611, F.614, S.779, N.782 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.508, A:L.611 Hydrogen bonds: A:N.782 GYK.6: 12 residues within 4Å: Chain A: I.602 Chain B: K.502, S.507, F.508, P.511, Y.607, L.611, F.614, L.778, S.779, N.782 Chain D: A.777 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.502, B:F.508, B:P.511, B:L.611, B:L.611, B:F.614 Hydrogen bonds: B:S.507, B:Y.607, B:N.782 GYK.8: 14 residues within 4Å: Chain A: S.776 Chain C: S.507, F.508, D.510, P.511, Y.607, L.611, F.614, M.620, L.778, S.779, N.782 Chain D: I.602, S.606 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.511, C:L.611, C:F.614 Hydrogen bonds: C:S.507, C:Y.607, D:S.606, D:S.606 pi-Stacking: C:F.614 GYK.10: 10 residues within 4Å: Chain D: S.507, F.508, D.510, P.511, Y.607, L.611, F.614, E.618, L.778, N.782 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.508, D:L.611, D:F.614, D:E.618 Hydrogen bonds: D:Y.607, D:N.782, D:N.782, B:S.606, B:S.606

4 x ZK1: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid(Non-covalent)

ZK1.5: 13 residues within 4Å: Chain A: E.393, Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.723 Hydrogen bonds: A:P.469, A:T.471, A:R.476, A:R.476, A:S.645, A:S.645, A:S.645 Halogen bonds: A:T.698 ZK1.7: 13 residues within 4Å: Chain B: E.393, Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.723 Hydrogen bonds: B:P.469, B:T.471, B:R.476, B:R.476, B:S.645, B:S.645 pi-Stacking: B:Y.441 Halogen bonds: B:T.698 ZK1.9: 12 residues within 4Å: Chain C: E.393, Y.396, Y.441, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.441, C:Y.723 Hydrogen bonds: C:T.471, C:T.471, C:T.471, C:R.476, C:R.476, C:S.645, C:S.645, C:S.645, C:T.677 Halogen bonds: C:E.393, C:T.698 ZK1.11: 13 residues within 4Å: Chain D: E.393, Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:P.469, D:T.471, D:T.471, D:R.476, D:R.476, D:S.645, D:S.645, D:T.677 Halogen bonds: D:T.698

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krintel, C. et al., Binding of a negative allosteric modulator and competitive antagonist can occur simultaneously at the ionotropic glutamate receptor GluA2. Febs J. (2021)

Release Date

2020-06-24

Peptides

Glutamate receptor 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 2