SMTL ID : 8ss9.1

Structure of LBD-TMD of AMPA receptor GluA2 in complex with auxiliary subunit TARP gamma-5 bound to competitive antagonist ZK and antiepileptic drug perampanel (closed state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.503, A:F.508, A:P.511, A:L.611, A:L.611, A:F.614, A:F.614, A:F.614, A:L.778, A:V.783 Hydrogen bonds: A:N.782 6ZP.9: 18 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, V.783 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:F.614, B:V.783 Hydrogen bonds: B:N.782 6ZP.15: 19 residues within 4Å: Chain B: S.606 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 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.503, C:F.508, C:L.611, C:L.611, C:F.614, C:L.778, C:N.782, C:V.783 Hydrogen bonds: C:N.782 pi-Stacking: C:F.614 6ZP.22: 17 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, V.783 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:P.503, D:F.508, D:P.511, D:L.611, D:L.611, D:F.614, D:F.614, D:N.782, D:V.783 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: 14 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, T.698, M.699, Y.723 10 PLIP interactions: 10 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 pi-Stacking: A:Y.441, A:Y.441 ZK1.10: 13 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, T.698, M.699, Y.723 9 PLIP interactions: 9 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 pi-Stacking: B:Y.441, B:Y.441 ZK1.16: 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 10 PLIP interactions: 10 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 pi-Stacking: C:Y.441, C:Y.441 ZK1.23: 13 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, T.698, M.699, Y.723 9 PLIP interactions: 9 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 pi-Stacking: D:Y.441, D:Y.441

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

PCW.3: 8 residues within 4Å: Chain A: V.505, Y.524, L.568, L.572, Y.788, I.789, L.796 Chain D: V.595 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.568, A:L.572, A:I.789, A:L.796, D:V.595 PCW.4: 10 residues within 4Å: Chain A: M.518, Y.854, K.993, Y.994, G.995, W.996, A.999, A.1002, I.1003 Ligands: PCW.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.994 PCW.5: 3 residues within 4Å: Chain A: P.921, F.922 Ligands: CLR.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.921, A:F.922 PCW.6: 14 residues within 4Å: Chain A: F.506, L.509, Y.514, W.517, M.518, I.520, V.521, F.522, Y.524, F.575, M.576, I.789 Chain D: F.598 Ligands: PCW.4 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.509, A:Y.514, A:Y.514, A:Y.514, A:W.517, A:M.518, A:V.521, A:V.521, A:F.522, A:Y.524, A:Y.524, A:F.575, A:I.789, D:F.598 PCW.11: 19 residues within 4Å: Chain A: I.591, G.594, V.595, F.598 Chain B: F.506, L.509, Y.514, W.517, I.520, V.521, Y.524, F.565, L.568, L.572, F.575, M.576, W.596, I.789 Ligands: PCW.12 18 PLIP interactions: 5 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:I.591, A:V.595, A:F.598, A:F.598, A:F.598, B:L.509, B:W.517, B:I.520, B:V.521, B:Y.524, B:Y.524, B:L.568, B:L.568, B:L.572, B:F.575, B:W.596, B:I.789 pi-Cation interactions: B:F.506 PCW.12: 11 residues within 4Å: Chain B: G.504, V.505, F.506, Y.788, I.789, G.792, G.793, L.796 Ligands: CLR.7, PCW.11, PCW.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.506, B:F.506, B:I.789, B:I.789 PCW.13: 2 residues within 4Å: Chain B: L.796 Ligands: PCW.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.796 PCW.17: 6 residues within 4Å: Chain B: V.595 Chain C: V.505, Y.524, L.568, L.572, L.796 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.568, C:L.572, C:L.796, B:V.595 PCW.18: 10 residues within 4Å: Chain C: M.518, Y.854, K.993, Y.994, G.995, W.996, A.999, A.1002, I.1003 Ligands: PCW.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.994, C:A.999, C:I.1003 PCW.19: 3 residues within 4Å: Chain C: P.921, F.922 Ligands: CLR.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.921, C:F.922, C:F.922 PCW.20: 11 residues within 4Å: Chain B: F.598 Chain C: F.506, L.509, Y.514, W.517, M.518, V.521, Y.524, F.575, M.576 Ligands: PCW.18 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.509, C:Y.514, C:Y.514, C:Y.514, C:W.517, C:M.518, C:V.521, C:V.521, C:Y.524, C:Y.524, C:F.575, B:F.598, B:F.598 PCW.24: 19 residues within 4Å: Chain C: R.590, I.591, G.594, V.595, F.598 Chain D: F.506, L.509, Y.514, W.517, I.520, V.521, Y.524, F.565, L.568, L.572, F.575, W.596, I.789 Ligands: PCW.25 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.509, D:I.520, D:V.521, D:Y.524, D:Y.524, D:L.568, D:L.572, D:L.572, D:F.575, D:F.575, D:W.596, D:I.789, C:I.591, C:V.595, C:F.598, C:F.598, C:F.598 pi-Cation interactions: D:F.506 PCW.25: 12 residues within 4Å: Chain C: V.595 Chain D: G.504, V.505, F.506, Y.788, I.789, G.792, G.793, L.796 Ligands: CLR.21, PCW.24, PCW.26 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.506, D:I.789, D:I.789, C:V.595 PCW.26: 2 residues within 4Å: Chain D: L.796 Ligands: PCW.25 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.796

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 8 residues within 4Å: Chain A: S.918, F.922, V.966, L.970 Chain B: Y.788, G.792 Ligands: PCW.5, PCW.12 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.788, A:F.922, A:F.922, A:V.966, A:L.970, A:L.970 CLR.21: 8 residues within 4Å: Chain C: M.915, S.918, V.966, L.970 Chain D: Y.788, G.792 Ligands: PCW.19, PCW.25 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.788, C:V.966, C:L.970, C:L.970

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

NA.8: 5 residues within 4Å: Chain A: T.616 Chain B: T.616 Chain C: A.612, T.616 Chain D: T.616 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.616 NA.14: 5 residues within 4Å: Chain A: Q.577 Chain B: Q.577 Chain C: Q.577, Q.578 Chain D: Q.577 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A: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

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, Voltage-dependent calcium channel gamma-5 subunit chimera

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