SMTL ID : 7ldd.1

native AMPA receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-mer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.63, S.65, D.66 Chain B: H.122 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.352, Q.354, N.363 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: Y.143, W.145, R.206, K.231, H.234, N.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.143, B:W.145, B:R.206 NAG-NAG.4: 4 residues within 4Å: Chain C: N.63, S.65, D.66 Chain D: H.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.352, Q.354, N.363 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: Y.143, W.145, R.206, K.231, H.234, N.256 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.143, D:W.145, D:R.206

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

ZK1.7: 11 residues within 4Å: Chain A: D.417, Y.419, Y.464, P.492, T.494, R.499, A.666, G.667, S.668, E.719, Y.746 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.464 Hydrogen bonds: A:P.492, A:T.494, A:R.499, A:A.666, A:S.668 Halogen bonds: A:D.417 ZK1.15: 13 residues within 4Å: Chain B: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, E.726, T.728, M.729, Y.753 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.499, B:T.501, B:R.506, B:R.506, B:S.675 ZK1.22: 11 residues within 4Å: Chain C: D.417, Y.419, Y.464, P.492, T.494, R.499, A.666, G.667, S.668, E.719, Y.746 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.464 Hydrogen bonds: C:P.492, C:T.494, C:R.499, C:A.666, C:S.668 Halogen bonds: C:D.417 ZK1.35: 13 residues within 4Å: Chain D: E.423, Y.426, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, E.726, T.728, M.729, Y.753 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.499, D:T.501, D:R.506, D:R.506, D:S.675

2 x R16: HEXADECANE(Non-covalent)

R16.8: 3 residues within 4Å: Chain A: V.528, Y.537 Ligands: OCT.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.528 R16.23: 3 residues within 4Å: Chain C: V.528, Y.537 Ligands: OCT.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.528

6 x OCT: N-OCTANE(Non-functional Binders)(Non-covalent)

OCT.9: 2 residues within 4Å: Ligands: R16.8, D12.30 No protein-ligand interaction detected (PLIP) OCT.20: 2 residues within 4Å: Chain B: F.562, I.594 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.562, B:I.594 OCT.24: 2 residues within 4Å: Ligands: D12.17, R16.23 No protein-ligand interaction detected (PLIP) OCT.33: 2 residues within 4Å: Chain D: F.562, I.594 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.562, D:I.594 OCT.45: 4 residues within 4Å: Chain A: I.548, I.587 Chain G: V.220 Ligands: HP6.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.548, A:I.587, A:I.587 OCT.51: 4 residues within 4Å: Chain C: I.548, I.587 Chain H: V.220 Ligands: HP6.29 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.548, C:I.587, C:I.587

4 x HP6: HEPTANE(Non-covalent)

HP6.10: 1 residues within 4Å: Chain A: F.588 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.588 HP6.14: 3 residues within 4Å: Chain A: I.587 Chain G: N.224 Ligands: OCT.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.587 HP6.25: 1 residues within 4Å: Chain C: F.588 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.588 HP6.29: 3 residues within 4Å: Chain C: I.587 Chain H: N.224 Ligands: OCT.51 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.587

6 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.11: 6 residues within 4Å: Chain A: L.532, Y.537, W.540, I.543, V.544 Ligands: D12.30 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.537, A:W.540, A:I.543, A:V.544 D10.26: 6 residues within 4Å: Chain C: L.532, Y.537, W.540, I.543, V.544 Ligands: D12.17 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.537, C:W.540, C:I.543, C:V.544 D10.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.39: 1 residues within 4Å: Chain F: W.88 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:W.88 D10.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NAG.12: 4 residues within 4Å: Chain A: E.197, G.225, N.249, K.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.249 NAG.13: 5 residues within 4Å: Chain A: N.257, T.259, D.260, H.367, K.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.367, A:K.378, A:K.378 NAG.16: 2 residues within 4Å: Chain B: N.359, N.370 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.370 NAG.27: 4 residues within 4Å: Chain C: E.197, G.225, N.249, K.372 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.249 NAG.28: 5 residues within 4Å: Chain C: N.257, T.259, D.260, H.367, K.378 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.367, C:K.378, C:K.378 NAG.36: 2 residues within 4Å: Chain D: N.359, N.370 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.370

6 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.17: 9 residues within 4Å: Chain B: I.621, G.624, V.625, F.628 Chain C: L.595, M.599, I.812 Ligands: OCT.24, D10.26 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.621, B:V.625, B:F.628, B:F.628, C:L.595, C:I.812 D12.30: 8 residues within 4Å: Chain A: L.595, I.812 Chain D: L.617, I.621, V.625, F.628 Ligands: OCT.9, D10.11 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.617, D:I.621, D:V.625, D:F.628, D:F.628, A:L.595, A:I.812, A:I.812 D12.42: 3 residues within 4Å: Chain G: F.32, W.87, I.136 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.32, G:W.87, G:W.87, G:I.136 D12.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.47: 3 residues within 4Å: Chain H: F.32, W.87, I.136 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:F.32, H:W.87, H:W.87, H:I.136 D12.48: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x C14: TETRADECANE(Non-covalent)(Non-functional Binders)

C14.18: 4 residues within 4Å: Chain A: G.617, F.621 Chain B: F.536, I.819 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.621, B:F.536, B:F.536, B:I.819, B:I.819 C14.31: 4 residues within 4Å: Chain C: G.617, F.621 Chain D: F.536, I.819 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.621, D:F.536, D:F.536, D:I.819, D:I.819 C14.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C14.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C14.46: 1 residues within 4Å: Chain G: F.106 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.106 C14.52: 1 residues within 4Å: Chain H: F.106 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.106

4 x DD9: nonane(Non-covalent)

DD9.19: 5 residues within 4Å: Chain A: F.621 Chain B: L.539, Y.544, W.547, F.605 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.539, B:Y.544, B:W.547, B:F.605, A:F.621 DD9.21: 2 residues within 4Å: Chain B: V.535, F.536 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.535, B:F.536 DD9.32: 5 residues within 4Å: Chain C: F.621 Chain D: L.539, Y.544, W.547, F.605 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.621, D:L.539, D:Y.544, D:W.547, D:F.605 DD9.34: 2 residues within 4Å: Chain D: V.535, F.536 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.535, D:F.536

2 x XVD: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol(Non-covalent)

XVD.44: 11 residues within 4Å: Chain A: Y.537, M.541, C.542, F.545 Chain G: M.35, N.172, V.176, I.180, F.205, G.208, G.209 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: G:F.205, A:M.541 Hydrogen bonds: G:N.172, G:N.172, G:F.205 pi-Stacking: A:F.545 XVD.50: 12 residues within 4Å: Chain C: Y.537, E.538, M.541, C.542, F.545 Chain H: M.35, N.172, V.176, I.180, F.205, G.208, G.209 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: H:F.205, C:M.541, C:F.545 Hydrogen bonds: H:N.172, H:N.172, H:F.205 pi-Stacking: C:F.545

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Nature (2021)

Release Date

2021-05-12

Peptides

Glutamate receptor 1: AC
Glutamate receptor: BD
Protein cornichon homolog 2: EF
Voltage-dependent calcium channel gamma-8 subunit: GH
11B8 scFv: IL
15F1 Fab light chain: JM
15F1 Fab heavy chain: KN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

H
H

I
I

L
L

J
J

M
M

K
K

N
N

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 1

Glutamate receptor

Protein cornichon homolog 2

Voltage-dependent calcium channel gamma-8 subunit

11B8 scFv

15F1 Fab light chain

15F1 Fab heavy chain

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