SMTL ID : 8fwu.1

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

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: 4 residues within 4Å: Chain A: R.543, N.546, L.729, T.730 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain B: R.543, N.546, R.748, N.749, C.750, N.751, E.806 Ligands: NAG-NAG-BMA-BMA.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.748, B:C.750 NAG-NAG.4: 4 residues within 4Å: Chain C: R.543, N.546, L.729, T.730 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.730 NAG-NAG.6: 8 residues within 4Å: Chain D: R.543, N.546, R.748, N.749, C.750, N.751, E.806 Ligands: NAG-NAG-BMA-BMA.5 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.748, D:C.750

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: 6 residues within 4Å: Chain B: R.543, N.546, T.548, L.729, T.730 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.5: 6 residues within 4Å: Chain D: R.543, N.546, T.548, L.729, T.730 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP)

4 x DNQ: 6,7-DINITROQUINOXALINE-2,3-DIONE(Non-covalent)

DNQ.7: 10 residues within 4Å: Chain A: E.440, Y.488, P.516, L.517, A.518, R.523, N.721, E.738, T.741, Y.764 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.440, A:A.518, A:R.523, A:R.523, A:E.738 pi-Stacking: A:Y.488, A:Y.488 DNQ.21: 9 residues within 4Å: Chain B: E.440, Y.488, P.516, L.517, A.518, R.523, N.721, T.741, Y.764 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.440, B:A.518, B:R.523, B:R.523 pi-Stacking: B:Y.488 DNQ.27: 9 residues within 4Å: Chain C: E.440, Y.488, P.516, L.517, A.518, R.523, N.721, E.738, Y.764 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.440, C:A.518, C:R.523, C:R.523, C:E.738 pi-Stacking: C:Y.488, C:Y.488 DNQ.40: 9 residues within 4Å: Chain D: E.440, Y.488, P.516, L.517, A.518, R.523, N.721, T.741, Y.764 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.440, D:A.518, D:R.523, D:R.523 pi-Stacking: D:Y.488

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

POV.8: 20 residues within 4Å: Chain A: P.550, G.551, F.553, L.556, N.557, W.564, L.568, C.571, L.572, F.612, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Chain D: F.642 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.9: 11 residues within 4Å: Chain A: F.553, L.568, W.613, V.616, I.825, A.829, L.833 Chain D: I.635, I.639 Ligands: POV.8, POV.11 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: V.552, V.817, Q.818, G.821, F.824, I.825, A.828, A.829, L.831, V.832, L.833, V.835 Chain D: Y.566, A.570 Ligand excluded by PLIP POV.11: 10 residues within 4Å: Chain A: L.608, L.609, F.612, L.833, F.836, V.837, G.840, Y.844 Ligands: POV.8, POV.9 Ligand excluded by PLIP POV.13: 13 residues within 4Å: Chain A: R.634, I.635, I.639 Chain B: F.553, L.568, L.609, V.616, A.829, G.830, L.833 Ligands: POV.14, POV.22, POV.23 Ligand excluded by PLIP POV.14: 13 residues within 4Å: Chain A: Y.587, L.631 Chain B: C.571, L.572, L.608, F.612, V.616, L.833, F.836, G.840, E.841 Ligands: POV.13, POV.22 Ligand excluded by PLIP POV.22: 22 residues within 4Å: Chain A: G.638, I.639, F.642, L.645 Chain B: P.550, G.551, V.552, F.553, L.556, P.561, W.564, M.565, L.568, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.13, POV.14 Ligand excluded by PLIP POV.23: 14 residues within 4Å: Chain A: Y.566 Chain B: V.552, V.817, Q.818, G.821, F.824, I.825, L.827, A.828, A.829, L.831, V.832, V.835 Ligands: POV.13 Ligand excluded by PLIP POV.28: 20 residues within 4Å: Chain B: I.639, F.642 Chain C: P.550, G.551, F.553, L.556, W.564, V.567, L.568, L.572, F.612, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.29, POV.31 Ligand excluded by PLIP POV.29: 13 residues within 4Å: Chain B: L.631, R.634, I.635, I.639 Chain C: F.553, L.568, W.613, V.616, I.825, A.829, L.833 Ligands: POV.28, POV.31 Ligand excluded by PLIP POV.30: 13 residues within 4Å: Chain B: Y.566 Chain C: V.552, V.817, Q.818, G.821, F.824, I.825, A.828, A.829, L.831, V.832, L.833, F.836 Ligand excluded by PLIP POV.31: 12 residues within 4Å: Chain B: Y.587 Chain C: L.608, L.609, F.612, L.833, F.836, V.837, G.840, E.841, Y.844 Ligands: POV.28, POV.29 Ligand excluded by PLIP POV.33: 23 residues within 4Å: Chain C: G.638, I.639, F.642, L.645 Chain D: P.550, G.551, V.552, F.553, S.554, L.556, P.561, W.564, M.565, L.568, V.616, L.619, M.620, I.647, I.648, Y.651, V.826 Ligands: POV.34, POV.35 Ligand excluded by PLIP POV.34: 15 residues within 4Å: Chain C: R.634, I.635, G.638, I.639 Chain D: F.553, L.568, L.609, W.613, V.616, V.826, A.829, G.830 Ligands: POV.33, POV.35, POV.41 Ligand excluded by PLIP POV.35: 14 residues within 4Å: Chain C: Y.587, L.631 Chain D: C.571, L.572, L.608, L.609, F.612, V.616, L.833, F.836, G.840, E.841 Ligands: POV.33, POV.34 Ligand excluded by PLIP POV.41: 12 residues within 4Å: Chain C: Y.566 Chain D: V.552, V.817, Q.818, G.821, F.824, I.825, A.828, A.829, L.831, V.832 Ligands: POV.34 Ligand excluded by PLIP

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

NAG.12: 4 residues within 4Å: Chain A: L.729, N.749, C.750, N.751 No protein-ligand interaction detected (PLIP) NAG.32: 4 residues within 4Å: Chain C: L.729, N.749, C.750, N.751 No protein-ligand interaction detected (PLIP)

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

NA.15: 4 residues within 4Å: Chain A: T.652 Chain B: T.652 Chain C: T.652 Chain D: T.652 No protein-ligand interaction detected (PLIP) NA.16: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.621 NA.17: 3 residues within 4Å: Chain B: A.656 Chain C: T.660 Chain D: A.656 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.656 NA.18: 3 residues within 4Å: Chain A: E.524, I.527, D.528 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.528, A:R.775 NA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.26: 4 residues within 4Å: Chain B: E.524, D.528, M.770 Chain C: I.780 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.524, B:D.528 NA.36: 3 residues within 4Å: Chain C: E.524, I.527, D.528 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.527, C:R.775 NA.42: 4 residues within 4Å: Chain A: I.780 Chain D: E.524, D.528, M.770 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.524, D:D.528

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

CL.19: 3 residues within 4Å: Chain A: K.531, R.775 Chain D: K.531 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain B: K.531 Chain C: K.531, R.775 Ligand excluded by PLIP

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

2J9.20: 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 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.532 Halogen bonds: C:M.534 2J9.24: 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 B, 2 interactions with chain C Hydrophobic interactions: B:P.532, C:T.535, C:L.791 Halogen bonds: B:M.534 2J9.38: 14 residues within 4Å: Chain A: K.531, P.532, F.533, 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 D, 2 interactions with chain A Hydrophobic interactions: D:P.532, A:T.535, A:L.791 Halogen bonds: D:M.534 2J9.39: 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.532 Halogen bonds: A:M.534

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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