SMTL ID : 8ss7.1

Structure of AMPA receptor GluA2 complex with auxiliary subunits TARP gamma-5 and cornichon-2 bound to competitive antagonist ZK, channel blocker spermidine and antiepileptic drug perampanel (closed state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

4 x 6ZP: 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile(Non-covalent)

6ZP.1: 19 residues within 4Å: Chain A: S.501, K.502, P.503, S.507, F.508, D.510, P.511, Y.607, N.610, L.611, F.614, L.615, L.778, N.782, V.783 Chain B: T.775, S.776, A.777 Chain D: S.606 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.508, A:P.511, A:L.611, A:L.611, A:F.614, A:F.614, A:L.778, A:V.783 Hydrogen bonds: A:N.782 pi-Stacking: A:F.614 6ZP.13: 17 residues within 4Å: Chain A: S.606 Chain B: S.501, K.502, P.503, S.507, F.508, D.510, P.511, Y.607, N.610, L.611, F.614, L.615, L.778, N.782 Chain C: S.776, A.777 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.508, B:P.511, B:L.611, B:L.611, B:F.614, B:F.614, B:L.778 Hydrogen bonds: B:N.782 pi-Stacking: B:F.614 6ZP.22: 18 residues within 4Å: Chain C: S.501, K.502, P.503, S.507, F.508, D.510, P.511, Y.607, N.610, L.611, F.614, L.615, L.778, N.782, V.783 Chain D: T.775, S.776, A.777 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.508, C:P.511, C:L.611, C:F.614, C:F.614, C:L.778, C:V.783 Hydrogen bonds: C:N.782 pi-Stacking: C:F.614 6ZP.33: 16 residues within 4Å: Chain A: S.776 Chain C: S.606 Chain D: S.501, K.502, P.503, S.507, F.508, D.510, P.511, Y.607, N.610, L.611, F.614, L.615, L.778, N.782 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.503, D:F.508, D:P.511, D:L.611, D:F.614, D:F.614 Hydrogen bonds: D:N.782 pi-Stacking: D:F.614

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

ZK1.2: 13 residues within 4Å: Chain A: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, E.696, M.699, Y.723 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:P.469, A:T.471, A:R.476, A:R.476, A:S.645, A:S.645, A:S.645, A:T.677, A:E.696 pi-Stacking: A:Y.441, A:Y.441 ZK1.14: 14 residues within 4Å: Chain B: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:P.469, B:T.471, B:R.476, B:R.476, B:S.645, B:S.645, B:S.645, B:E.696 pi-Stacking: B:Y.441, B:Y.441 ZK1.23: 13 residues within 4Å: Chain C: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, E.696, M.699, Y.723 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:P.469, C:T.471, C:R.476, C:R.476, C:S.645, C:S.645, C:S.645, C:T.677, C:E.696 pi-Stacking: C:Y.441, C:Y.441 ZK1.34: 14 residues within 4Å: Chain D: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:P.469, D:T.471, D:R.476, D:R.476, D:S.645, D:S.645, D:S.645, D:E.696 pi-Stacking: D:Y.441, D:Y.441

28 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

PCW.3: 14 residues within 4Å: Chain A: K.502, P.503, G.504, V.505, F.506, Y.788, I.789, G.792, G.793, L.796 Chain D: V.595 Ligands: PCW.6, CLR.7, PCW.32 Ligand excluded by PLIP PCW.4: 14 residues within 4Å: Chain A: M.518, F.522, Y.524, L.572, Y.854, K.993, Y.994, G.995, W.996, A.999, I.1003 Ligands: PCW.5, PCW.6, PCW.32 Ligand excluded by PLIP PCW.5: 17 residues within 4Å: Chain A: I.525, V.529, R.536, N.560, E.561, G.563, F.565, N.566, F.835, L.1006, S.1010, V.1013, M.1014, Y.1017 Ligands: PCW.4, CLR.8, PCW.32 Ligand excluded by PLIP PCW.6: 13 residues within 4Å: Chain A: F.506, Y.514, E.515, W.517, I.520, Y.524, F.575, Y.992, Y.994 Chain D: F.598 Ligands: PCW.3, PCW.4, PCW.32 Ligand excluded by PLIP PCW.9: 18 residues within 4Å: Chain A: P.539, R.585, L.587, R.590, G.594, V.595, F.598 Chain B: Y.524, F.565, L.568, L.572, M.576, I.789 Ligands: PCW.15, PCW.16, PCW.17, CLR.20, PCW.44 Ligand excluded by PLIP PCW.10: 3 residues within 4Å: Chain A: V.952, I.955 Ligands: PCW.18 Ligand excluded by PLIP PCW.15: 13 residues within 4Å: Chain A: V.595 Chain B: K.502, G.504, V.505, F.506, Y.788, I.789, G.792, L.796, L.799 Ligands: PCW.9, PCW.17, CLR.19 Ligand excluded by PLIP PCW.16: 18 residues within 4Å: Chain B: F.522, Y.524, I.525, V.529, F.532, R.536, N.560, G.563, I.564, F.565, L.568 Chain F: P.70, S.73, I.74, L.77, L.80 Ligands: PCW.9, PCW.44 Ligand excluded by PLIP PCW.17: 16 residues within 4Å: Chain A: F.598 Chain B: F.506, Y.514, E.515, W.517, M.518, I.520, V.521, Y.524, L.572, F.575, M.576, I.789 Ligands: PCW.9, PCW.15, PCW.44 Ligand excluded by PLIP PCW.18: 10 residues within 4Å: Chain A: L.533, F.537, I.955, L.959 Chain B: M.798, L.799, A.801, L.802, F.805 Ligands: PCW.10 Ligand excluded by PLIP PCW.21: 20 residues within 4Å: Chain B: Y.540, R.585, S.586, L.587, R.590, I.591, G.594, V.595, F.598 Chain C: Y.524, F.565, L.568, W.569, L.572, I.789 Ligands: PCW.24, PCW.25, PCW.26, PCW.27, CLR.29 Ligand excluded by PLIP PCW.24: 12 residues within 4Å: Chain B: V.595 Chain C: K.502, P.503, G.504, V.505, F.506, G.792, G.793, L.796 Ligands: PCW.21, PCW.27, CLR.28 Ligand excluded by PLIP PCW.25: 15 residues within 4Å: Chain C: M.518, F.522, Y.524, L.572, Y.854, K.993, Y.994, G.995, W.996, A.999, A.1002, I.1003 Ligands: PCW.21, PCW.26, PCW.27 Ligand excluded by PLIP PCW.26: 19 residues within 4Å: Chain C: I.525, V.529, R.536, N.560, E.561, G.563, I.564, F.565, N.566, F.835, L.1006, E.1009, S.1010, V.1013, M.1014, Y.1017 Ligands: PCW.21, PCW.25, CLR.29 Ligand excluded by PLIP PCW.27: 13 residues within 4Å: Chain B: F.598 Chain C: F.506, Y.514, E.515, W.517, I.520, Y.524, F.575, Y.992, Y.994 Ligands: PCW.21, PCW.24, PCW.25 Ligand excluded by PLIP PCW.30: 17 residues within 4Å: Chain C: P.539, R.585, L.587, R.590, G.594, V.595, F.598 Chain D: Y.524, F.565, L.568, W.569, L.572, I.789 Ligands: PCW.35, PCW.36, PCW.37, CLR.40 Ligand excluded by PLIP PCW.31: 3 residues within 4Å: Chain C: V.952, I.955 Ligands: PCW.38 Ligand excluded by PLIP PCW.32: 21 residues within 4Å: Chain A: Y.524, F.565, L.568, W.569, L.572, M.576, I.789 Chain D: Y.540, R.585, S.586, L.587, R.590, I.591, G.594, V.595, F.598 Ligands: PCW.3, PCW.4, PCW.5, PCW.6, CLR.8 Ligand excluded by PLIP PCW.35: 12 residues within 4Å: Chain C: V.595 Chain D: K.502, G.504, V.505, F.506, Y.788, I.789, G.792, L.799 Ligands: PCW.30, PCW.37, CLR.39 Ligand excluded by PLIP PCW.36: 17 residues within 4Å: Chain D: F.522, I.525, V.529, F.532, R.536, N.560, G.563, I.564, F.565, L.568 Chain E: V.69, P.70, S.73, I.74, L.80 Ligands: PCW.30, PCW.43 Ligand excluded by PLIP PCW.37: 16 residues within 4Å: Chain C: F.598 Chain D: F.506, Y.514, E.515, W.517, M.518, I.520, V.521, Y.524, L.572, F.575, M.576, I.789 Ligands: PCW.30, PCW.35, PCW.43 Ligand excluded by PLIP PCW.38: 10 residues within 4Å: Chain C: L.533, F.537, I.955, L.959 Chain D: M.798, L.799, A.801, L.802, F.805 Ligands: PCW.31 Ligand excluded by PLIP PCW.41: 8 residues within 4Å: Chain A: G.795, M.798, L.799, A.801, L.802 Chain D: L.533 Chain E: A.18, F.22 Ligand excluded by PLIP PCW.42: 3 residues within 4Å: Chain E: L.150, V.154 Ligands: CLR.7 Ligand excluded by PLIP PCW.43: 9 residues within 4Å: Chain D: M.518, Y.524 Chain E: L.80, L.83, C.84, A.86, W.88 Ligands: PCW.36, PCW.37 Ligand excluded by PLIP PCW.44: 9 residues within 4Å: Chain B: M.518, Y.524 Chain F: L.80, L.83, C.84, A.86 Ligands: PCW.9, PCW.16, PCW.17 Ligand excluded by PLIP PCW.45: 9 residues within 4Å: Chain B: L.533 Chain C: G.795, M.798, L.799, A.801, L.802 Chain F: A.18, S.19, F.22 Ligand excluded by PLIP PCW.46: 1 residues within 4Å: Ligands: CLR.28 Ligand excluded by PLIP

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 8 residues within 4Å: Chain A: V.505, Y.788, V.791 Chain E: L.14, M.153, L.157 Ligands: PCW.3, PCW.42 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:L.14, E:L.157, A:Y.788, A:Y.788 CLR.8: 5 residues within 4Å: Chain A: I.803, Y.807, K.808 Ligands: PCW.5, PCW.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.807, A:Y.807 CLR.19: 8 residues within 4Å: Chain A: F.922, V.966, L.970 Chain B: Y.788, V.791, G.792, G.795 Ligands: PCW.15 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.922, A:V.966, A:V.966, A:L.970, B:Y.788, B:Y.788, B:Y.788 CLR.20: 7 residues within 4Å: Chain A: L.587 Chain B: V.800, I.803, E.804, Y.807, K.808 Ligands: PCW.9 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.587, B:V.800, B:I.803, B:E.804, B:Y.807 CLR.28: 8 residues within 4Å: Chain C: V.505, Y.788, V.791 Chain F: L.14, M.153, L.157 Ligands: PCW.24, PCW.46 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:Y.788, C:Y.788, C:V.791, F:L.14, F:L.157 CLR.29: 5 residues within 4Å: Chain C: I.803, Y.807, K.808 Ligands: PCW.21, PCW.26 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.807, C:Y.807 CLR.39: 8 residues within 4Å: Chain C: V.966, L.970 Chain D: V.505, Y.788, V.791, G.792, G.795 Ligands: PCW.35 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.505, D:Y.788, D:Y.788, C:V.966, C:V.966, C:L.970 CLR.40: 6 residues within 4Å: Chain C: L.587 Chain D: I.803, E.804, Y.807, K.808 Ligands: PCW.30 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.803, D:E.804, D:Y.807, C:L.587

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: A.612, T.616 Chain B: T.616 Chain C: A.612, T.616 Chain D: T.616 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.616

1 x SPD: SPERMIDINE(Non-covalent)

SPD.12: 8 residues within 4Å: Chain A: Q.577, G.579 Chain B: Q.577, G.579 Chain C: Q.577, G.579 Chain D: Q.577, G.579 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.579, B:Q.577, B:Q.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Modulation of GluA2-gamma 5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-09-06

Peptides

Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera: ABCD
Protein cornichon homolog 2: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera

Protein cornichon homolog 2

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