SMTL ID : 9dxs.1

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Spermine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 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: 3 residues within 4Å: Chain A: R.543, N.751 Ligands: NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: R.543, N.751 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.5, NAG-NAG-BMA-BMA.5 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.2: 5 residues within 4Å: Chain B: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.5: 5 residues within 4Å: Chain D: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP)

4 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.7: 15 residues within 4Å: Chain A: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Chain D: I.519, P.532, M.534, T.535, S.761, K.762, G.763 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:T.535, A:L.791, D:P.532 Halogen bonds: D:M.534 2J9.17: 13 residues within 4Å: Chain B: K.531, P.532, F.533, T.535, L.783, Q.786 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.532, B:T.535 Halogen bonds: C:M.534 2J9.20: 15 residues within 4Å: Chain B: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain C: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.535, C:L.791, B:P.532 Halogen bonds: B:M.534 2J9.30: 13 residues within 4Å: Chain A: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain D: K.531, P.532, F.533, T.535, L.783, Q.786 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.535, A:P.532 Halogen bonds: A:M.534

12 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.8: 13 residues within 4Å: Chain A: F.553, L.556, P.561, W.564, L.568, L.619, M.620, V.826 Chain D: I.639, F.642, L.645 Ligands: POV.9, POV.10 16 PLIP interactions: 6 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:I.639, D:F.642, D:F.642, D:F.642, D:F.642, D:L.645, A:F.553, A:F.553, A:L.556, A:P.561, A:W.564, A:W.564, A:W.564, A:L.568, A:L.619, A:V.826 POV.9: 4 residues within 4Å: Chain A: A.829, L.833 Ligands: POV.8, CLR.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.829, A:L.833 POV.10: 6 residues within 4Å: Chain A: R.583, F.612 Chain B: K.870 Chain D: L.631 Ligands: POV.8, CLR.29 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:L.631, A:F.612, B:K.870, B:K.870 POV.15: 6 residues within 4Å: Chain A: K.870 Chain D: C.576, R.583, L.608, Y.844 Ligands: CLR.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.870, D:L.608 Salt bridges: A:K.870 POV.18: 14 residues within 4Å: Chain A: G.638, I.639, F.642, L.645 Chain B: F.553, L.556, P.561, W.564, L.568, V.616, L.619, M.620, V.826 Ligands: POV.19 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.553, B:L.556, B:P.561, B:W.564, B:W.564, B:W.564, B:L.568, B:V.616, B:L.619, A:I.639, A:F.642, A:F.642, A:F.642, A:L.645 Hydrogen bonds: B:F.553 POV.19: 9 residues within 4Å: Chain A: L.631, R.634, I.635 Chain B: F.553, W.613, A.829, L.833 Ligands: CLR.14, POV.18 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.613, B:A.829, B:L.833, A:L.631 POV.22: 5 residues within 4Å: Chain B: C.576, R.583, Y.844 Chain C: K.870 Ligands: CLR.13 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.870 Salt bridges: C:K.870 POV.23: 14 residues within 4Å: Chain B: I.639, F.642, L.645 Chain C: F.553, L.556, P.561, W.564, L.568, M.620, I.647, I.648, V.826 Ligands: POV.24, POV.25 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.553, C:F.553, C:L.556, C:L.556, C:P.561, C:W.564, C:W.564, C:L.568, C:I.647, C:I.648, C:V.826, B:I.639, B:F.642, B:F.642, B:F.642, B:F.642, B:L.645 POV.24: 4 residues within 4Å: Chain C: V.826, A.829 Ligands: POV.23, CLR.26 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.826, C:A.829 POV.25: 9 residues within 4Å: Chain B: L.631, G.638 Chain C: R.583, F.612, W.613, V.616 Chain D: K.870 Ligands: CLR.21, POV.23 7 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:L.631, C:F.612, C:F.612, C:W.613, C:V.616, D:K.870, D:K.870 POV.31: 12 residues within 4Å: Chain C: F.642, L.645 Chain D: F.553, L.556, P.561, W.564, V.567, L.568, V.616, M.620, V.826 Ligands: POV.32 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.553, D:L.556, D:P.561, D:P.561, D:W.564, D:W.564, D:W.564, D:V.567, D:L.568, D:V.616, C:F.642, C:F.642, C:L.645 Hydrogen bonds: D:F.553 POV.32: 7 residues within 4Å: Chain C: L.631, I.635 Chain D: F.553, A.829, L.833 Ligands: POV.31, CLR.33 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.829, D:L.833, C:L.631

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 3 residues within 4Å: Chain A: F.824, I.825 Ligands: POV.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.824, A:I.825 CLR.13: 5 residues within 4Å: Chain A: Y.587, L.631 Chain B: E.841, Y.844 Ligands: POV.22 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.587, A:Y.587, A:L.631, B:E.841, B:Y.844, B:Y.844 CLR.14: 3 residues within 4Å: Chain A: Y.566 Chain B: F.824 Ligands: POV.19 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.566, A:Y.566, B:F.824 CLR.21: 6 residues within 4Å: Chain B: Y.587, L.631 Chain C: L.609, E.841, Y.844 Ligands: POV.25 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.587, B:L.631, C:L.609, C:E.841, C:Y.844, C:Y.844 CLR.26: 2 residues within 4Å: Chain C: F.824 Ligands: POV.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.824, C:F.824 CLR.28: 5 residues within 4Å: Chain C: Y.587, L.631 Chain D: E.841, Y.844 Ligands: POV.15 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:E.841, D:Y.844, C:Y.587, C:Y.587, C:L.631 CLR.29: 6 residues within 4Å: Chain A: G.840, E.841, Y.844 Chain D: Y.587, L.631 Ligands: POV.10 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.587, D:L.631, A:E.841, A:Y.844 CLR.33: 3 residues within 4Å: Chain C: Y.566 Chain D: F.824 Ligands: POV.32 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.824, D:F.824, C:Y.566, C:Y.566

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

NAG.12: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.543 NAG.27: 3 residues within 4Å: Chain C: R.543, N.546 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.543

1 x SPM: SPERMINE(Non-covalent)

SPM.16: 9 residues within 4Å: Chain A: Q.621, Q.622, S.624, E.625 Chain B: Q.621, Q.622 Chain C: Q.621, Q.622 Chain D: Q.621 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.621

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels. Nat Commun (2024)

Release Date

2024-12-11

Peptides

Glutamate receptor ionotropic, kainate 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 ionotropic, kainate 2

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