SMTL ID : 8fws.1

Structure of the ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with the positive allosteric modulator BPAM344

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: N.546, L.729, T.730 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: R.543, R.748, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.748 NAG-NAG.4: 3 residues within 4Å: Chain C: N.546, L.729, T.730 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: R.543, R.748, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.5 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.748

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 2J9.15: 14 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, M.534, T.535, L.783, Q.786 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:P.532, D:T.535, D:Q.786 Halogen bonds: A:M.534 2J9.24: 14 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:P.532, B:T.535, B:Q.786 Halogen bonds: C:M.534 2J9.25: 14 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 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.535, B:P.532 Halogen bonds: B:M.534

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

POV.8: 19 residues within 4Å: Chain A: P.550, G.551, F.553, L.556, N.557, W.564, L.568, L.572, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Chain D: I.639, F.642, L.645 Ligands: POV.9 Ligand excluded by PLIP POV.9: 9 residues within 4Å: Chain A: F.553, L.568, V.826, A.829, L.833 Chain D: I.639 Ligands: POV.8, POV.10, POV.11 Ligand excluded by PLIP POV.10: 12 residues within 4Å: Chain A: V.552, V.817, Q.818, G.821, F.824, I.825, L.827, A.828, A.829, L.831 Chain D: Y.566 Ligands: POV.9 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain A: L.609, F.612, L.833, F.836, G.840 Chain D: Y.587 Ligands: POV.9 Ligand excluded by PLIP POV.13: 12 residues within 4Å: Chain A: R.634, I.635, I.639 Chain B: F.553, L.568, L.609, W.613, V.826, A.829, L.833 Ligands: POV.14, POV.20 Ligand excluded by PLIP POV.14: 13 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.568, L.572, L.608, L.609, F.612, L.833, F.836, E.841, Y.844 Ligands: POV.13, POV.21 Ligand excluded by PLIP POV.20: 21 residues within 4Å: Chain A: G.638, I.639, F.642, L.645 Chain B: P.550, G.551, F.553, L.556, P.561, W.564, M.565, L.568, C.571, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.13 Ligand excluded by PLIP POV.21: 11 residues within 4Å: Chain A: Y.566, G.573, V.577 Chain B: V.552, V.817, Q.818, F.824, I.825, L.827, L.833 Ligands: POV.14 Ligand excluded by PLIP POV.22: 10 residues within 4Å: Chain B: Y.587, A.630 Chain C: L.608, L.609, F.612, L.833, F.836, G.840 Ligands: POV.26, POV.27 Ligand excluded by PLIP POV.26: 21 residues within 4Å: Chain B: I.639, F.642, L.645 Chain C: P.550, G.551, F.553, L.556, N.557, W.564, L.568, L.572, F.612, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.22, POV.27 Ligand excluded by PLIP POV.27: 12 residues within 4Å: Chain B: I.635, G.638, I.639 Chain C: F.553, L.568, W.613, V.616, V.826, A.829 Ligands: POV.22, POV.26, POV.28 Ligand excluded by PLIP POV.28: 12 residues within 4Å: Chain B: Y.566 Chain C: V.552, V.817, Q.818, G.821, F.824, I.825, L.827, A.828, A.829, L.831 Ligands: POV.27 Ligand excluded by PLIP POV.30: 13 residues within 4Å: Chain C: Y.587, L.631 Chain D: L.568, L.572, L.608, L.609, F.612, L.833, F.836, E.841, Y.844 Ligands: POV.34, POV.35 Ligand excluded by PLIP POV.33: 21 residues within 4Å: Chain C: I.639, F.642, L.645 Chain D: P.550, G.551, F.553, L.556, N.557, P.561, W.564, M.565, L.568, C.571, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.34 Ligand excluded by PLIP POV.34: 13 residues within 4Å: Chain C: R.634, I.635, I.639 Chain D: F.553, L.568, L.609, W.613, V.616, V.826, A.829, L.833 Ligands: POV.30, POV.33 Ligand excluded by PLIP POV.35: 12 residues within 4Å: Chain C: Y.566, V.577 Chain D: V.552, V.817, Q.818, G.821, F.824, I.825, L.827, A.829, L.833 Ligands: POV.30 Ligand excluded by PLIP

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

NAG.12: 3 residues within 4Å: Chain A: N.749, C.750, N.751 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain C: N.749, C.750, N.751 No protein-ligand interaction detected (PLIP)

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

NA.16: 3 residues within 4Å: Chain A: Q.621 Chain B: Q.621 Chain D: Q.621 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.621 NA.17: 4 residues within 4Å: Chain A: T.652, A.656 Chain B: T.652 Chain C: T.652 No protein-ligand interaction detected (PLIP) NA.18: 4 residues within 4Å: Chain A: E.524, I.527, D.528, M.770 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.528 NA.23: 4 residues within 4Å: Chain B: E.524, I.527, D.528, M.770 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.524 NA.31: 3 residues within 4Å: Chain C: E.524, D.528, M.770 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.527 NA.36: 4 residues within 4Å: Chain D: E.524, I.527, D.528, M.770 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.524

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.19: 3 residues within 4Å: Chain A: K.531, R.775, T.779 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain C: K.531, R.775, T.779 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Positive and negative allosteric modulation of GluK2 kainate receptors by BPAM344 and antiepileptic perampanel. Cell Rep (2023)

Release Date

2023-04-19

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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