SMTL ID : 7rz4.1

Structure of the complex of AMPA receptor GluA2 with auxiliary subunit TARP gamma-5 bound to competitive antagonist ZK 200775

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

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: 10 residues within 4Å: Chain A: Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, 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 ZK1.9: 13 residues within 4Å: Chain B: E.393, Y.396, Y.441, P.469, 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 ZK1.17: 11 residues within 4Å: Chain C: E.393, Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, M.699, Y.723 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.441 Hydrogen bonds: C:P.469, C:T.471, C:R.476, C:R.476, C:S.645, C:S.645, C:T.677 pi-Stacking: C:Y.441 Halogen bonds: C:E.393 ZK1.26: 12 residues within 4Å: Chain D: E.393, Y.396, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, E.696, 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 pi-Stacking: D:Y.441, D:Y.441 Halogen bonds: D:E.696

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: Q.328, N.335, K.337, N.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.328, A:N.335, A:K.337 NAG.10: 4 residues within 4Å: Chain B: Q.328, N.335, N.346, T.348 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.348 Hydrogen bonds: B:Q.328 NAG.18: 3 residues within 4Å: Chain C: N.335, K.337, N.346 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.335, C:K.337 NAG.27: 3 residues within 4Å: Chain D: Q.328, N.335, N.346 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.328

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

PCW.3: 10 residues within 4Å: Chain A: F.506, L.509, I.789, G.792, G.793, L.796 Chain D: R.590, G.594, V.595 Ligands: PCW.4 Ligand excluded by PLIP PCW.4: 7 residues within 4Å: Chain A: Y.514, M.518, V.521, F.522, Y.992, F.998 Ligands: PCW.3 Ligand excluded by PLIP PCW.5: 6 residues within 4Å: Chain A: R.536, G.563, I.564, F.565, L.1006, Y.1017 Ligand excluded by PLIP PCW.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.7: 1 residues within 4Å: Chain A: Y.788 Ligand excluded by PLIP PCW.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.11: 11 residues within 4Å: Chain A: R.590 Chain B: Y.514, W.517, M.518, I.520, V.521, Y.524, W.569, L.572, F.575 Ligands: PCW.12 Ligand excluded by PLIP PCW.12: 6 residues within 4Å: Chain A: I.591 Chain B: F.506, L.509, Y.514, I.789 Ligands: PCW.11 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Chain B: F.565, N.566, L.568, E.804 Ligand excluded by PLIP PCW.14: 2 residues within 4Å: Chain B: F.506 Ligands: PCW.15 Ligand excluded by PLIP PCW.15: 4 residues within 4Å: Chain B: Y.788, V.791, G.795 Ligands: PCW.14 Ligand excluded by PLIP PCW.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.19: 5 residues within 4Å: Chain C: F.506, G.792, G.793, L.796 Ligands: PCW.20 Ligand excluded by PLIP PCW.20: 9 residues within 4Å: Chain C: Y.514, M.518, F.522, Y.992, F.998, A.999, A.1002, I.1003 Ligands: PCW.19 Ligand excluded by PLIP PCW.21: 8 residues within 4Å: Chain C: F.532, R.536, I.564, F.565, L.1006, S.1010, M.1014, Y.1017 Ligand excluded by PLIP PCW.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.23: 2 residues within 4Å: Chain C: Y.788, V.791 Ligand excluded by PLIP PCW.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.25: 1 residues within 4Å: Chain D: F.522 Ligand excluded by PLIP PCW.28: 9 residues within 4Å: Chain C: R.590, I.591 Chain D: Y.514, M.518, V.521, Y.524, L.572, F.575 Ligands: PCW.29 Ligand excluded by PLIP PCW.29: 5 residues within 4Å: Chain C: I.591 Chain D: F.506, Y.514, I.789 Ligands: PCW.28 Ligand excluded by PLIP PCW.30: 6 residues within 4Å: Chain C: L.587 Chain D: F.565, L.568, I.803, E.804, Y.807 Ligand excluded by PLIP PCW.31: 1 residues within 4Å: Ligands: PCW.32 Ligand excluded by PLIP PCW.32: 1 residues within 4Å: Ligands: PCW.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klykov, O. et al., Structure and desensitization of AMPA receptor complexes with type II TARP gamma 5 and GSG1L. Mol.Cell (2021)

Release Date

2021-10-27

Peptides

Glutamate receptor 2: 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

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