SMTL ID : 6ucb.1

GluA2 in complex with its auxiliary subunit CNIH3 - with antagonist ZK200775, LBD, TMD, CNIH3, and lipids

Coordinates

PDB Format Compare

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: 16 residues within 4Å: Chain A: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, T.707, L.725, E.726, M.729, Y.753 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.471 Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:S.675, A:T.707 pi-Stacking: A:Y.471 Halogen bonds: A:E.423 ZK1.5: 18 residues within 4Å: Chain B: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, T.707, L.725, E.726, T.728, M.729, K.751, Y.753 10 PLIP interactions: 10 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:S.675, B:T.707 pi-Stacking: B:Y.471, B:Y.471 ZK1.12: 16 residues within 4Å: Chain C: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, T.707, L.725, E.726, M.729, Y.753 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.471 Hydrogen bonds: C:P.499, C:T.501, C:R.506, C:R.506, C:S.675, C:T.707 pi-Stacking: C:Y.471 Halogen bonds: C:E.423 ZK1.25: 18 residues within 4Å: Chain H: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, T.707, L.725, E.726, T.728, M.729, K.751, Y.753 11 PLIP interactions: 11 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:S.675, H:T.707 pi-Stacking: H:Y.471, H:Y.471 Halogen bonds: H:T.728

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

OLC.2: 11 residues within 4Å: Chain A: Y.544, M.548, V.551, I.555 Chain E: I.80, C.84, Q.86 Ligands: PAM.3, PAM.18, PAM.19, OLC.26 No protein-ligand interaction detected (PLIP) OLC.6: 20 residues within 4Å: Chain B: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Chain C: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 Chain G: L.69, S.73 Ligands: OLC.13, PAM.14, PAM.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.554, C:Y.554, C:I.555, C:V.559 Hydrogen bonds: C:R.566 OLC.7: 20 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 F: L.69, S.73 Ligands: OLC.8, PAM.9, PAM.20 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: B:V.551, B:Y.554, B:Y.554, B:I.555, A:I.621, F:L.69 Hydrogen bonds: B:R.566 OLC.8: 10 residues within 4Å: Chain B: Y.544, M.548, V.551, I.555 Chain F: I.80, C.84, Q.86 Ligands: OLC.7, PAM.9, PAM.20 No protein-ligand interaction detected (PLIP) OLC.13: 11 residues within 4Å: Chain C: Y.544, M.548, V.551, I.555 Chain G: I.80, C.84, Q.86 Ligands: OLC.6, PAM.14, PAM.22, PAM.23 No protein-ligand interaction detected (PLIP) OLC.26: 20 residues within 4Å: Chain A: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 Chain E: L.69, S.73 Chain H: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Ligands: OLC.2, PAM.3, PAM.19 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:Y.554, A:Y.554, A:V.559, A:F.562, H:I.621 OLC.27: 20 residues within 4Å: Chain C: S.616, L.617, R.620, I.621, G.624, V.625, W.627, F.628 Chain D: L.69, S.73 Chain H: V.551, Y.554, I.555, S.558, V.559, F.562, R.566 Ligands: PAM.16, OLC.28, PAM.29 7 PLIP interactions: 4 interactions with chain H, 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: H:Y.554, H:I.555, H:F.562, D:L.69, C:I.621, C:I.621 Hydrogen bonds: H:R.566 OLC.28: 10 residues within 4Å: Chain D: I.80, C.84, Q.86 Chain H: Y.544, M.548, V.551, I.555 Ligands: PAM.16, OLC.27, PAM.29 No protein-ligand interaction detected (PLIP)

14 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.3: 11 residues within 4Å: Chain A: F.536, L.539, I.819, G.822, G.823, L.826 Chain H: V.625 Ligands: OLC.2, PAM.4, PAM.19, OLC.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.536 PAM.4: 8 residues within 4Å: Chain A: G.534, V.535, F.536, Y.818, I.819, G.822 Ligands: PAM.3, CLR.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.535, A:F.536, A:F.536 Hydrogen bonds: A:V.535, A:F.536 PAM.9: 11 residues within 4Å: Chain A: I.621 Chain B: F.536, L.539, I.819, G.822, G.823, L.826 Ligands: OLC.7, OLC.8, PAM.10, PAM.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.536, B:I.819 PAM.10: 8 residues within 4Å: Chain B: G.534, V.535, F.536, Y.818, I.819, G.822 Ligands: PAM.9, CLR.11 No protein-ligand interaction detected (PLIP) PAM.14: 12 residues within 4Å: Chain B: I.621, V.625 Chain C: F.536, L.539, I.819, G.822, G.823, L.826 Ligands: OLC.6, OLC.13, PAM.15, PAM.23 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.536 PAM.15: 8 residues within 4Å: Chain C: G.534, V.535, F.536, Y.818, I.819, G.822 Ligands: PAM.14, CLR.21 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.535, C:F.536 Hydrogen bonds: C:V.535, C:F.536 PAM.16: 15 residues within 4Å: Chain C: V.625, F.628 Chain D: C.84, A.85, Q.86 Chain H: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Ligands: OLC.27, OLC.28, PAM.29 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:Y.544, H:V.551, H:I.819, C:F.628 PAM.18: 7 residues within 4Å: Chain E: I.80, L.83, C.84, Q.86, W.88 Ligands: OLC.2, PAM.19 No protein-ligand interaction detected (PLIP) PAM.19: 15 residues within 4Å: Chain A: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Chain E: C.84, Q.86 Chain H: V.625, F.628 Ligands: OLC.2, PAM.3, PAM.18, OLC.26 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: A:Y.544, A:W.547, A:V.551, H:F.628 Hydrogen bonds: E:Q.86 PAM.20: 15 residues within 4Å: Chain A: V.625, F.628 Chain B: L.539, Y.544, W.547, M.548, V.551, I.819 Chain F: F.5, C.84, A.85, Q.86 Ligands: OLC.7, OLC.8, PAM.9 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: A:F.628, B:Y.544, B:V.551 Hydrogen bonds: F:Q.86 PAM.22: 7 residues within 4Å: Chain G: I.80, L.83, C.84, Q.86, W.88 Ligands: OLC.13, PAM.23 No protein-ligand interaction detected (PLIP) PAM.23: 15 residues within 4Å: Chain B: V.625, F.628 Chain C: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Chain G: C.84, Q.86 Ligands: OLC.6, OLC.13, PAM.14, PAM.22 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: G:Q.86 Hydrophobic interactions: B:F.628, C:Y.544, C:W.547, C:V.551 PAM.29: 11 residues within 4Å: Chain C: I.621 Chain H: F.536, L.539, I.819, G.822, G.823, L.826 Ligands: PAM.16, OLC.27, OLC.28, PAM.30 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.536, H:I.819 PAM.30: 8 residues within 4Å: Chain H: G.534, V.535, F.536, Y.818, I.819, G.822 Ligands: CLR.24, PAM.29 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:V.535, H:F.536, H:F.536

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 16 residues within 4Å: Chain B: Y.818, V.821, G.822, G.825, M.828, L.829, L.832 Chain E: M.11, L.14, V.15, A.18, F.146, L.150, M.153, L.157 Ligands: PAM.10 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:L.14, E:A.18, E:L.157, B:L.829 CLR.17: 15 residues within 4Å: Chain A: Y.818, V.821, G.822, G.825, M.828, L.829, L.832 Chain D: M.11, L.14, V.15, A.18, F.146, M.153, L.157 Ligands: PAM.4 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.14, D:V.15, D:A.18, D:L.157 Hydrogen bonds: A:Y.818 CLR.21: 15 residues within 4Å: Chain C: Y.818, V.821, G.822, G.825, M.828, L.829, L.832 Chain F: M.11, L.14, V.15, A.18, F.146, M.153, L.157 Ligands: PAM.15 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.14, F:L.157 CLR.24: 15 residues within 4Å: Chain G: M.11, L.14, V.15, A.18, F.146, M.153, L.157 Chain H: Y.818, V.821, G.822, G.825, M.828, L.829, L.832 Ligands: PAM.30 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:M.11, G:L.14, G:A.18, G:L.157, H:L.829

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: ABCH
Protein cornichon homolog 3: DEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

H
D

D
E

E
F

F
G

G
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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