SMTL ID : 6dm1.1

Open state GluA2 in complex with STZ and blocked by NASPM, after micelle signal subtraction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 10 residues within 4Å: Chain A: Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.646, E.696, Y.723 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.441, A:Y.441 Hydrogen bonds: A:T.471, A:G.644, A:S.645, A:S.645, A:T.646, A:E.696, A:E.696, E.1 Salt bridges: A:R.476 GLU.3: 10 residues within 4Å: Chain B: Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.646, E.696, Y.723 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.441, B:Y.441 Hydrogen bonds: B:P.469, B:T.471, B:G.644, B:S.645, B:T.646, B:K.647, B:E.696, B:E.696, E.3 Salt bridges: B:R.476, B:K.721 GLU.5: 10 residues within 4Å: Chain C: Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.646, E.696, Y.723 11 PLIP interactions: 1 Ligand-Ligand interactions, 10 interactions with chain C Hydrogen bonds: E.5, C:T.471, C:G.644, C:S.645, C:S.645, C:T.646, C:E.696, C:E.696 Hydrophobic interactions: C:Y.441, C:Y.441 Salt bridges: C:R.476 GLU.8: 10 residues within 4Å: Chain D: Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.646, E.696, Y.723 13 PLIP interactions: 12 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.441, D:Y.441 Hydrogen bonds: D:P.469, D:T.471, D:G.644, D:S.645, D:T.646, D:K.647, D:E.696, D:E.696, E.8 Salt bridges: D:R.476, D:K.721

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 12 residues within 4Å: Chain A: P.485, F.486, M.487, S.488, L.742, S.745, D.751, K.754 Chain D: I.472, S.720, K.721, G.722 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.742, D:I.472 Hydrogen bonds: A:S.488, A:S.488, A:K.754, A:K.754, D:S.720 Halogen bonds: A:D.751 CYZ.4: 14 residues within 4Å: Chain B: P.485, F.486, M.487, S.488, L.742, S.745, L.750, D.751, K.754 Chain C: I.472, P.485, S.720, K.721, G.722 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.742, B:L.750, C:I.472, C:P.485 Hydrogen bonds: B:S.488, B:K.754, B:K.754, C:S.720 Halogen bonds: B:D.751 CYZ.6: 12 residues within 4Å: Chain B: I.472, S.720, K.721, G.722 Chain C: P.485, F.486, M.487, S.488, L.742, S.745, D.751, K.754 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.742, B:I.472 Hydrogen bonds: C:S.488, C:S.488, C:K.754, C:K.754, B:S.720 Halogen bonds: C:D.751 CYZ.9: 14 residues within 4Å: Chain A: I.472, P.485, S.720, K.721, G.722 Chain D: P.485, F.486, M.487, S.488, L.742, S.745, L.750, D.751, K.754 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.742, D:L.750, A:I.472, A:I.472, A:P.485 Hydrogen bonds: D:S.488, D:K.754, D:K.754, A:S.720 Halogen bonds: D:D.751

1 x GYY: N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2-(naphthalen-1-yl)acetamide(Non-covalent)

GYY.7: 19 residues within 4Å: Chain A: Q.577, Q.578, G.579, C.580 Chain B: Q.577, Q.578, G.579, C.580, T.608 Chain C: Q.577, Q.578, G.579, C.580, D.581 Chain D: Q.577, G.579, C.580, D.581, T.608 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.577, D:D.581 Hydrophobic interactions: C:Q.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Twomey, E.C. et al., Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors. Neuron (2018)

Release Date

2018-08-22

Peptides

Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit: 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-2 subunit

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