SMTL ID : 9dxq.1

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Philanthotoxin-74

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

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: 5 residues within 4Å: Chain A: R.543, N.546, T.730 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: R.543, N.751 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: R.543, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.3, NAG-NAG-BMA-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: R.543, N.546, T.730 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: R.543, N.751 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: R.543, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.7, NAG-NAG-BMA-BMA.7 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.3: 5 residues within 4Å: Chain B: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.7: 5 residues within 4Å: Chain D: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.8 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)

2J9.9: 13 residues within 4Å: Chain A: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Chain D: I.519, P.532, T.535, S.761, K.762, G.763 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.532 2J9.21: 15 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 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:T.535, B:L.791, C:P.532 Halogen bonds: C:M.534, C:T.535 2J9.29: 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 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.532 Halogen bonds: B:M.534 2J9.43: 15 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 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:T.535, D:L.791, A:P.532 Halogen bonds: A:M.534, A:T.535

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

POV.10: 15 residues within 4Å: Chain A: G.551, F.553, L.556, N.557, P.561, W.564, L.619, M.620, I.648, Y.651 Chain D: G.638, I.639, F.642 Ligands: POV.11, POV.12 Ligand excluded by PLIP POV.11: 8 residues within 4Å: Chain A: F.553, W.613, V.616, V.826 Chain D: L.631, I.639 Ligands: POV.10, POV.12 Ligand excluded by PLIP POV.12: 5 residues within 4Å: Chain A: P.561, L.568, L.569 Ligands: POV.10, POV.11 Ligand excluded by PLIP POV.15: 8 residues within 4Å: Chain A: L.869, K.870, C.871 Chain D: F.579, R.583, L.608, Y.844 Ligands: CLR.36 Ligand excluded by PLIP POV.20: 7 residues within 4Å: Chain A: F.579, V.580, R.583 Chain B: M.867, K.870, Q.872 Ligands: CLR.41 Ligand excluded by PLIP POV.22: 18 residues within 4Å: Chain A: G.638, I.639, F.642 Chain B: P.550, G.551, F.553, S.554, L.556, P.561, W.564, M.565, L.568, L.619, M.620, Y.651, V.826 Ligands: POV.23, POV.24 Ligand excluded by PLIP POV.23: 8 residues within 4Å: Chain A: L.631, R.634, I.635 Chain B: F.553, I.825, L.833 Ligands: POV.22, POV.24 Ligand excluded by PLIP POV.24: 4 residues within 4Å: Chain B: M.565, L.568 Ligands: POV.22, POV.23 Ligand excluded by PLIP POV.28: 6 residues within 4Å: Chain B: R.583, Y.844 Chain C: L.869, K.870, C.871 Ligands: CLR.14 Ligand excluded by PLIP POV.30: 15 residues within 4Å: Chain B: G.638, I.639, F.642, L.645 Chain C: G.551, F.553, L.556, N.557, P.561, W.564, L.619, M.620, Y.651 Ligands: POV.31, POV.32 Ligand excluded by PLIP POV.31: 8 residues within 4Å: Chain B: L.631, I.639 Chain C: F.553, W.613, V.826, A.829 Ligands: POV.30, POV.32 Ligand excluded by PLIP POV.32: 3 residues within 4Å: Chain C: L.568 Ligands: POV.30, POV.31 Ligand excluded by PLIP POV.34: 19 residues within 4Å: Chain C: G.638, I.639, F.642, L.645 Chain D: P.550, G.551, F.553, S.554, L.556, P.561, W.564, L.568, L.619, M.620, I.648, Y.651, V.826 Ligands: POV.35, POV.44 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain C: L.631, R.634, I.635, I.639 Chain D: F.553, W.613, I.825, V.826, L.833 Ligands: POV.34, POV.44 Ligand excluded by PLIP POV.42: 7 residues within 4Å: Chain C: F.579, R.583, Y.844 Chain D: M.867, K.870, Q.872 Ligands: CLR.26 Ligand excluded by PLIP POV.44: 5 residues within 4Å: Chain D: M.565, L.568, L.569 Ligands: POV.34, POV.35 Ligand excluded by PLIP

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.13: 5 residues within 4Å: Chain A: V.817, F.824, I.825, L.827 Chain D: L.569 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.817, A:F.824, A:I.825, A:L.827 CLR.14: 4 residues within 4Å: Chain A: Y.587, L.631 Chain B: Y.844 Ligands: POV.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.631, B:Y.844 CLR.25: 1 residues within 4Å: Chain B: F.824 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.824 CLR.26: 6 residues within 4Å: Chain B: Y.587, L.631 Chain C: V.837, E.841, Y.844 Ligands: POV.42 7 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:Q.872 Hydrophobic interactions: B:Y.587, B:Y.587, B:L.631, C:V.837, C:E.841, C:Y.844 CLR.33: 3 residues within 4Å: Chain C: V.817, F.824, I.825 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.817, C:F.824, C:I.825 CLR.36: 5 residues within 4Å: Chain C: Y.587, L.631 Chain D: G.840, Y.844 Ligands: POV.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.844, D:Y.844, C:Y.587, C:L.631 CLR.37: 3 residues within 4Å: Chain C: Y.566 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.41: 6 residues within 4Å: Chain A: V.837, E.841, Y.844 Chain B: Q.872 Chain D: L.631 Ligands: POV.20 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:V.837, A:E.841, A:Y.844, D:L.631 Hydrogen bonds: B:Q.872

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

NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.17: 4 residues within 4Å: Chain A: T.660 Chain B: T.660 Chain C: T.660 Chain D: T.660 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.660 NA.18: 4 residues within 4Å: Chain A: E.524, I.527, D.528, M.770 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.524, A:E.524 NA.27: 3 residues within 4Å: Chain B: E.524, I.527, D.528 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.524, B:I.527 NA.39: 4 residues within 4Å: Chain C: E.524, I.527, D.528, M.770 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.524, C:I.527 NA.45: 3 residues within 4Å: Chain D: E.524, I.527, D.528 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.524, D:I.527

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.40: 3 residues within 4Å: Chain B: K.531 Chain C: K.531, R.775 Ligand excluded by PLIP

1 x 01: N-{7-[(4-aminobutyl)amino]heptyl}-Nalpha-butanoyl-D-tyrosinamide

01.38: 15 residues within 4Å: Chain A: Q.621, S.649, T.652 Chain B: Q.621, Q.622, I.648, T.652 Chain C: Q.621, S.624, L.645, I.648, S.649 Chain D: Q.621, Q.622, S.624 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:I.648, B:T.652, C:L.645, D:Q.621 Hydrogen bonds: B:Q.622, C:S.624, C:L.645, D: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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