SMTL ID : 9dxt.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

2J9.1: 13 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, K.762, G.763 Ligands: 2J9.9 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:P.532, A:T.535, A:L.791 Hydrogen bonds: A:K.531 2J9.9: 16 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, L.791 Ligands: 2J9.1 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.535, D:L.791, A:P.532 Halogen bonds: A:M.534 2J9.13: 16 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Ligands: 2J9.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.535, B:L.791, C:P.532 Halogen bonds: C:M.534 2J9.24: 14 residues within 4Å: Chain B: I.519, P.532, M.534, K.762, G.763 Chain C: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Ligands: 2J9.13 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.535, C:L.791, B:P.532 Hydrogen bonds: C:K.531 Halogen bonds: B:M.534

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

POV.2: 13 residues within 4Å: Chain A: F.553, L.556, P.561, W.564, L.568, L.619, M.620, I.648, V.826, A.829 Chain D: I.639, F.642, L.645 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: 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:I.648, A:V.826, A:A.829, D:I.639, D:F.642, D:F.642, D:L.645 POV.10: 11 residues within 4Å: Chain A: S.868, L.869, K.870, C.871, Q.872 Chain D: C.576, F.579, R.583, T.607, L.608 Ligands: CLR.30 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.579, D:L.608, A:K.870, A:Q.872 Hydrogen bonds: A:Q.872 POV.11: 10 residues within 4Å: Chain A: C.576, F.579, R.583, F.584, T.607, L.608 Chain B: M.867, K.870, Q.872 Ligands: CLR.12 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.579, A:R.583, A:F.584, A:F.584, A:L.608, B:K.870, B:K.870 POV.14: 12 residues within 4Å: Chain A: G.638, I.639, F.642 Chain B: F.553, L.556, N.557, P.561, W.564, M.565, L.619, M.620, A.829 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.642, B:F.553, B:P.561, B:W.564, B:L.619, B:A.829 POV.23: 11 residues within 4Å: Chain B: C.576, F.579, R.583, T.607, L.608 Chain C: S.868, L.869, K.870, C.871, Q.872 Ligands: CLR.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.579, B:L.608, C:K.870 Hydrogen bonds: C:Q.872 POV.25: 13 residues within 4Å: Chain B: I.639, F.642, L.645 Chain C: F.553, L.556, P.561, W.564, L.568, L.619, M.620, I.648, V.826, A.829 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.553, C:L.556, C:P.561, C:W.564, C:W.564, C:W.564, C:L.568, C:L.619, C:I.648, C:V.826, C:A.829, B:I.639, B:F.642, B:F.642, B:L.645 POV.33: 10 residues within 4Å: Chain C: C.576, F.579, R.583, F.584, T.607, L.608 Chain D: M.867, K.870, Q.872 Ligands: CLR.21 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.579, C:R.583, C:F.584, C:F.584, C:L.608, D:K.870, D:K.870 POV.34: 14 residues within 4Å: Chain C: G.638, I.639, F.642 Chain D: F.553, L.556, N.557, P.561, W.564, M.565, V.567, L.568, L.619, M.620, A.829 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.553, D:P.561, D:W.564, D:V.567, D:L.568, D:L.619, D:A.829, C:F.642

16 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.3: 4 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.4, NAG.5 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Ligands: NAG.3 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: R.543, C.750, N.751 Ligands: NAG.3, NAG.6 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Ligands: NAG.5 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain B: R.543, N.546, T.548 Ligands: NAG.16, NAG.19 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain B: R.543, T.730 Ligands: NAG.15, AH2.17, AH2.18, NAG.19 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain B: R.543, N.751 Ligands: NAG.15, NAG.16, NAG.20 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Ligands: NAG.19 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: R.543, N.546 Ligands: NAG.27, NAG.28 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: R.543, C.750, N.751 Ligands: NAG.26, NAG.29 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Ligands: NAG.28 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain D: R.543, N.546, T.548 Ligands: NAG.36, NAG.39 Ligand excluded by PLIP NAG.36: 7 residues within 4Å: Chain D: R.543, L.729, T.730 Ligands: NAG.35, AH2.37, AH2.38, NAG.39 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain D: R.543, N.751 Ligands: NAG.35, NAG.36, NAG.40 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Ligands: NAG.39 Ligand excluded by PLIP

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 5 residues within 4Å: Chain A: Y.587 Chain B: L.609, E.841, Y.844 Ligands: POV.23 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.609, B:E.841, B:Y.844, A:Y.587 CLR.8: 4 residues within 4Å: Chain A: Y.566, G.573 Chain B: V.817, F.824 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.817, B:F.824, A:Y.566, A:Y.566 CLR.12: 6 residues within 4Å: Chain A: E.841, Y.844 Chain B: Q.872 Chain D: Y.587, L.631 Ligands: POV.11 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.631, A:Y.844 CLR.21: 6 residues within 4Å: Chain B: Y.587, L.631 Chain C: E.841, Y.844 Chain D: Q.872 Ligands: POV.33 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.631, C:Y.844 CLR.22: 5 residues within 4Å: Chain B: Y.566, A.570 Chain C: V.817, I.825, L.827 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.817, C:I.825, C:L.827, B:Y.566, B:A.570 CLR.30: 6 residues within 4Å: Chain C: Y.587, L.631 Chain D: L.609, E.841, Y.844 Ligands: POV.10 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.609, D:E.841, D:Y.844, C:Y.587, C:L.631 CLR.31: 4 residues within 4Å: Chain C: Y.566, G.573 Chain D: V.817, F.824 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.817, D:F.824, C:Y.566, C:Y.566 CLR.32: 5 residues within 4Å: Chain A: V.817, I.825, L.827 Chain D: Y.566, A.570 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.566, D:A.570, A:V.817, A:I.825, A:L.827

4 x AH2: 1-deoxy-alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

AH2.17: 3 residues within 4Å: Chain B: T.730 Ligands: NAG.16, AH2.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.730 AH2.18: 2 residues within 4Å: Ligands: NAG.16, AH2.17 No protein-ligand interaction detected (PLIP) AH2.37: 3 residues within 4Å: Chain D: T.730 Ligands: NAG.36, AH2.38 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.730 AH2.38: 2 residues within 4Å: Ligands: NAG.36, AH2.37 No protein-ligand interaction detected (PLIP)

1 x 01: N,N'-[butane-1,4-diylbis(azanediylpropane-3,1-diyl)]bis[3-(3,4-dihydroxyphenyl)propanamide]

01.41: 15 residues within 4Å: Chain A: Q.621, G.623, T.652 Chain B: Q.621, Q.622, E.625 Chain C: Q.621, G.623, S.624, E.625, M.627 Chain D: Q.621, Q.622, S.624, E.625 12 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:E.625, A:Q.621, B:Q.621, B:E.625, D:E.625 Hydrogen bonds: C:Q.621, C:T.652, C:T.652, A:G.623, A:T.652, B:E.625, D:E.625

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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