SMTL ID : 9dxr.1

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Nephilatoxin-8

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: 4 residues within 4Å: Chain A: R.543, N.546 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: 5 residues within 4Å: Chain B: R.543, N.749, C.750, N.751 Ligands: 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: 5 residues within 4Å: Chain D: 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: 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 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:P.532, A:L.791 Halogen bonds: D:M.534 2J9.16: 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 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 2J9.19: 13 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, S.761, K.762, G.763 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.535, B:L.791, C:P.532 2J9.21: 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 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.532, C:L.791 Halogen bonds: B:M.534

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: F.553, L.556, P.561, W.564, L.568, L.619, M.620, I.647, I.648, Y.651, V.826 Chain D: I.639, F.642, L.645 Ligands: POV.11 Ligand excluded by PLIP POV.11: 6 residues within 4Å: Chain A: F.553, V.826, A.829, L.833 Chain D: R.634 Ligands: POV.10 Ligand excluded by PLIP POV.12: 6 residues within 4Å: Chain A: V.552, V.817, F.824, V.832 Chain D: Y.566, L.569 Ligand excluded by PLIP POV.13: 10 residues within 4Å: Chain A: L.631, R.634, I.639 Chain B: F.553, L.568, L.609, F.612, A.829, L.833 Ligands: POV.20 Ligand excluded by PLIP POV.14: 6 residues within 4Å: Chain A: Y.566, L.569 Chain B: G.821, F.824, I.825, A.828 Ligand excluded by PLIP POV.15: 5 residues within 4Å: Chain A: Y.587 Chain B: L.833, F.836, Y.844 Chain C: Q.872 Ligand excluded by PLIP POV.18: 8 residues within 4Å: Chain A: L.609, F.612, G.840 Chain B: Q.872, R.873 Chain D: Y.587, Y.590, K.629 Ligand excluded by PLIP POV.20: 17 residues within 4Å: Chain A: I.639, F.642, L.645 Chain B: P.550, F.553, L.556, N.557, P.561, W.564, V.567, L.568, V.616, L.619, M.620, I.647, V.826 Ligands: POV.13 Ligand excluded by PLIP POV.22: 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.647, I.648 Ligands: POV.23 Ligand excluded by PLIP POV.23: 6 residues within 4Å: Chain B: R.634 Chain C: F.553, V.826, A.829, L.833 Ligands: POV.22 Ligand excluded by PLIP POV.24: 6 residues within 4Å: Chain B: Y.566, L.569 Chain C: V.552, V.817, F.824, V.832 Ligand excluded by PLIP POV.25: 7 residues within 4Å: Chain B: Y.587, Y.590, K.629 Chain C: L.609, F.612, G.840 Chain D: Q.872 Ligand excluded by PLIP POV.26: 9 residues within 4Å: Chain C: L.631, R.634 Chain D: F.553, L.568, L.609, I.825, A.829, L.833 Ligands: POV.28 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain C: Y.566, L.569, L.572 Chain D: V.817, G.821, F.824, I.825, A.828 Ligand excluded by PLIP POV.28: 16 residues within 4Å: Chain C: I.639, F.642, L.645 Chain D: P.550, F.553, L.556, N.557, P.561, W.564, L.568, V.616, L.619, M.620, I.647, V.826 Ligands: POV.26 Ligand excluded by PLIP POV.29: 6 residues within 4Å: Chain A: Q.872 Chain C: Y.587 Chain D: L.609, L.833, F.836, G.840 Ligand excluded by PLIP

1 x 01: N~1~-{5-[(N-{4-[(3-aminopropyl)amino]butyl}-beta-alanyl)amino]pentyl}-N~2~-[(1H-indol-3-yl)acetyl]-D-aspartamide

01.17: 22 residues within 4Å: Chain A: Q.621, G.623, I.648, T.652 Chain B: Q.621, Q.622, S.624, E.625, M.627, I.648, S.649 Chain C: Q.621, G.623, E.625, I.648, S.649, T.652 Chain D: Q.621, Q.622, I.648, S.649, T.652 9 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: D:I.648, C:I.648, A:Q.621, A:T.652 Hydrogen bonds: D:Q.622, D:T.652, B:Q.621, A:Q.621, A:G.623

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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