SMTL ID : 6peq.1

GluA2 in complex with its auxiliary subunit CNIH3 - map LBD-TMD-C3 - with antagonist ZK200775 -without NTD

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: 14 residues within 4Å: Chain A: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, L.725, E.726, M.729, Y.753 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.499, A:T.501, A:R.506, A:R.506, A:S.675, A:S.675 pi-Stacking: A:Y.471 ZK1.6: 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, M.729, K.751, 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 ZK1.18: 14 residues within 4Å: Chain G: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, L.725, E.726, M.729, Y.753 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:P.499, G:T.501, G:R.506, G:R.506, G:S.675, G:S.675 pi-Stacking: G:Y.471 ZK1.24: 16 residues within 4Å: Chain H: 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, K.751, Y.753 9 PLIP interactions: 9 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

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

OLC.2: 10 residues within 4Å: Chain A: Y.544, M.548, V.551, F.552 Chain D: I.80, C.84 Ligands: PAM.3, PAM.4, PAM.14, OLC.26 No protein-ligand interaction detected (PLIP) OLC.7: 11 residues within 4Å: Chain B: Y.544, E.545, M.548, V.551, F.552, I.555 Chain E: I.80, C.84 Ligands: OLC.8, PAM.9, PAM.10 No protein-ligand interaction detected (PLIP) OLC.8: 19 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 Ligands: OLC.7, PAM.9 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: E:L.69, A:I.621, B:Y.554, B:Y.554 OLC.19: 11 residues within 4Å: Chain F: I.80, C.84, Q.86 Chain G: Y.544, M.548, V.551, F.552 Ligands: PAM.17, OLC.20, PAM.21, PAM.22 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.551 OLC.20: 20 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 Ligands: OLC.19, PAM.21, PAM.22 6 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: G:Y.554, G:V.559, F:L.69, B:L.617, B:I.621 Salt bridges: B:R.620 OLC.25: 13 residues within 4Å: Chain C: I.80, C.84, Q.86 Chain G: L.617, I.621 Chain H: Y.544, M.548, V.551, F.552, I.555 Ligands: OLC.27, PAM.28, PAM.29 No protein-ligand interaction detected (PLIP) OLC.26: 18 residues within 4Å: Chain A: V.551, Y.554, I.555, S.558, V.559, F.562 Chain D: 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 6 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: D:L.69, A:Y.554, A:Y.554, A:V.559, A:F.562, H:I.621 OLC.27: 19 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 Ligands: OLC.25, PAM.28 7 PLIP interactions: 5 interactions with chain H, 1 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: H:Y.554, H:Y.554, H:F.562, C:L.69, G:I.621 Hydrogen bonds: H:R.566, H:R.566

14 x PAM: PALMITOLEIC ACID(Non-covalent)(Non-functional Binders)

PAM.3: 13 residues within 4Å: Chain A: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Chain D: Q.86 Chain H: V.625, F.628 Ligands: OLC.2, PAM.4, OLC.26 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:Y.544, A:Y.544, A:V.551, H:F.628 PAM.4: 9 residues within 4Å: Chain A: F.536, L.539, Y.544, I.819, G.822, G.823 Ligands: OLC.2, PAM.3, PAM.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.536 PAM.5: 7 residues within 4Å: Chain A: V.535, F.536, Y.818, I.819, G.822 Ligands: PAM.4, CLR.12 No protein-ligand interaction detected (PLIP) PAM.9: 14 residues within 4Å: Chain A: V.625, F.628 Chain B: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Chain E: C.84, Q.86 Ligands: OLC.7, OLC.8, PAM.10 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.628, B:Y.544, B:Y.544, B:V.551, B:I.819 PAM.10: 10 residues within 4Å: Chain B: F.536, L.539, Y.544, I.819, G.822, G.823, L.826 Ligands: OLC.7, PAM.9, PAM.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.536, B:Y.544, B:I.819 PAM.11: 8 residues within 4Å: Chain B: G.534, V.535, F.536, Y.818, I.819, G.822 Ligands: PAM.10, CLR.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.535, B:F.536 PAM.14: 6 residues within 4Å: Chain D: I.80, L.83, C.84, Q.86, W.88 Ligands: OLC.2 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.80 PAM.17: 7 residues within 4Å: Chain F: I.80, L.83, C.84, Q.86, W.88 Ligands: OLC.19, PAM.21 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.80 PAM.21: 14 residues within 4Å: Chain B: V.625, F.628 Chain F: Q.86 Chain G: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Ligands: PAM.17, OLC.19, OLC.20, PAM.22 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:F.628, G:Y.544, G:Y.544, G:W.547 PAM.22: 12 residues within 4Å: Chain B: V.625 Chain G: F.536, L.539, Y.544, I.819, G.822, G.823, L.826 Ligands: OLC.19, OLC.20, PAM.21, PAM.23 No protein-ligand interaction detected (PLIP) PAM.23: 7 residues within 4Å: Chain G: V.535, F.536, Y.818, I.819, G.822 Ligands: CLR.15, PAM.22 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.536, G:F.536 PAM.28: 13 residues within 4Å: Chain C: F.5 Chain G: V.625, F.628 Chain H: L.539, Y.544, E.545, W.547, M.548, V.551, I.819 Ligands: OLC.25, OLC.27, PAM.29 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:Y.544, H:Y.544, H:W.547, H:V.551, H:I.819, G:F.628 PAM.29: 10 residues within 4Å: Chain H: F.536, L.539, Y.544, I.819, G.822, G.823, L.826 Ligands: OLC.25, PAM.28, PAM.30 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.536, H:I.819 PAM.30: 7 residues within 4Å: Chain H: V.535, F.536, Y.818, I.819, G.822 Ligands: CLR.16, PAM.29 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:V.535, H:F.536

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.12: 16 residues within 4Å: Chain A: Y.818, V.821, G.822, G.825, M.828, L.829, L.832 Chain C: M.11, L.14, V.15, A.18, L.150, M.153, I.154, L.157 Ligands: PAM.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.18, C:L.157, A:Y.818 Hydrogen bonds: A:Y.818 CLR.13: 14 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, F.146, M.153, L.157 Ligands: PAM.11 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.14, D:V.15, D:L.157, B:Y.818 CLR.15: 14 residues within 4Å: Chain E: M.11, L.14, V.15, A.18, F.146, M.153, L.157 Chain G: Y.818, V.821, G.822, G.825, M.828, L.829 Ligands: PAM.23 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain E Hydrophobic interactions: G:Y.818, E:L.14, E:V.15, E:A.18, E:L.157 Hydrogen bonds: G:Y.818 CLR.16: 14 residues within 4Å: Chain F: 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 Ligands: PAM.30 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:A.18, F:L.157, H:Y.818, H:Y.818

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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