SMTL ID : 6ud4.1

GluA2 in complex with its auxiliary subunit CNIH3 in AS map II - (LBD-TMD-C3(AS) II)- with antagonist ZK200775, without NTD

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

ZK1.1: 15 residues within 4Å: Chain A: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, T.707, L.725, E.726, M.729, Y.753 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.499 Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:S.675, A:S.675, A:S.675, A:S.675, A:T.707 pi-Stacking: A:Y.471 ZK1.4: 16 residues within 4Å: Chain B: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, T.707, L.725, E.726, T.728, M.729, Y.753 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:P.499, B:T.501, B:R.506, B:R.506, B:S.675, B:S.675, B:T.707 pi-Stacking: B:Y.471, B:Y.471 ZK1.9: 15 residues within 4Å: Chain G: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, T.707, L.725, E.726, M.729, Y.753 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:P.499 Hydrogen bonds: G:P.499, G:T.501, G:R.506, G:R.506, G:S.675, G:S.675, G:S.675, G:S.675, G:T.707 pi-Stacking: G:Y.471 ZK1.11: 14 residues within 4Å: Chain H: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, E.726, T.728, M.729, Y.753 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:P.499, H:T.501, H:R.506, H:R.506, H:S.675, H:S.675, H:T.707 pi-Stacking: H:Y.471, H:Y.471 Halogen bonds: H:T.728

4 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 18 residues within 4Å: Chain A: I.550, V.551, Y.554, I.555, S.558, V.559, F.562, R.566 Chain D: L.69, S.73 Chain H: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: A:Y.554, A:I.555, A:V.559, A:F.562, A:F.562, H:I.621, H:F.628, D:L.69 OLC.5: 17 residues within 4Å: Chain A: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Chain B: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 Chain E: L.69, S.73 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:I.621, B:Y.554, B:Y.554, B:F.562, B:F.562, E:L.69 OLC.10: 17 residues within 4Å: Chain B: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Chain F: L.69, S.73 Chain G: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 7 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: B:I.621, F:L.69, G:Y.554, G:V.559, G:F.562, G:F.562 Hydrogen bonds: G:R.566 OLC.12: 17 residues within 4Å: Chain C: L.69, S.73 Chain G: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Chain H: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:L.69, H:Y.554, H:Y.554, H:F.562, H:F.562, G:I.621

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 13 residues within 4Å: Chain A: Y.818, V.821, G.822, G.825, L.826, M.828, L.829 Chain C: M.11, L.14, V.15, A.18, M.153, L.157 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.818, A:Y.818, A:V.821, A:L.829, C:A.18 Hydrogen bonds: A:Y.818 CLR.6: 12 residues within 4Å: Chain B: Y.818, V.821, G.822, G.825, M.828, L.829 Chain D: M.11, L.14, V.15, A.18, M.153, L.157 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.14, D:A.18, D:L.157, B:Y.818, B:V.821 CLR.7: 13 residues within 4Å: Chain E: M.11, L.14, V.15, A.18, M.153, L.157 Chain G: Y.818, V.821, G.822, G.825, L.826, M.828, L.829 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:L.14, E:V.15, E:A.18, E:L.157, G:L.829 Hydrogen bonds: G:Y.818, G:Y.818 CLR.8: 14 residues within 4Å: Chain F: M.11, L.14, V.15, A.18, F.146, M.153, I.154, L.157 Chain H: Y.818, V.821, G.822, G.825, M.828, L.829 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain F Hydrogen bonds: H:Y.818 Hydrophobic interactions: F:L.14, F:A.18, F:L.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakagawa, T., Structures of the AMPA receptor in complex with its auxiliary subunit cornichon. Science (2019)

Release Date

2019-12-04

Peptides

Glutamate receptor 2: ABGH
Protein cornichon homolog 3: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G
C

H
D

C
E

D
F

E
G

F
H

Membrane

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

Protein cornichon homolog 3

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