SMTL ID : 9n4s.1

Composite map for GluK2-1xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 10 residues within 4Å: Chain A: S.154, R.158, L.161, D.162, R.194, Y.195, N.378, T.380, N.381, T.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158 NAG-NAG-BMA-MAN-MAN.4: 8 residues within 4Å: Chain B: S.154, R.158, D.162, N.378, N.381, T.385, P.407, S.409 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.158, B:R.158 NAG-NAG-BMA-MAN-MAN.6: 6 residues within 4Å: Chain C: R.158, D.162, Y.195, N.378, N.381, T.385 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.158, C:R.158, C:R.158 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain D: D.152, S.154, R.158, D.162, R.194, N.378, N.381, L.383, T.385, W.405, G.410 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.194, D:R.158

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain B: F.167, G.273, V.274, N.275, S.393, K.395, K.418, G.419, K.420 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.418, B:K.420 NAG-NAG.8: 4 residues within 4Å: Chain D: G.273, V.274, N.275, S.393 No protein-ligand interaction detected (PLIP)

3 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.5: 4 residues within 4Å: Chain B: R.543, N.546, T.730 Ligands: NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.7: 5 residues within 4Å: Chain C: R.543, N.546, T.730, D.732 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.10: 5 residues within 4Å: Chain D: R.543, N.546, L.729, T.730 Ligands: NAG.53 No protein-ligand interaction detected (PLIP)

4 x KAI: 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE(Non-covalent)

KAI.11: 12 residues within 4Å: Chain A: E.440, Y.488, P.516, A.518, R.523, V.685, G.688, A.689, T.690, N.721, L.736, E.738 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.488, A:V.685 Hydrogen bonds: A:A.518, A:A.689, A:T.690, A:T.690, A:N.721, A:E.738 Salt bridges: A:R.523, A:K.762 KAI.24: 11 residues within 4Å: Chain B: E.440, Y.488, P.516, A.518, R.523, V.685, G.688, A.689, T.690, N.721, E.738 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.488, B:V.685 Hydrogen bonds: B:A.518, B:A.689, B:T.690, B:T.690 Salt bridges: B:R.523 KAI.34: 10 residues within 4Å: Chain C: E.440, Y.488, P.516, A.518, R.523, V.685, A.689, T.690, N.721, E.738 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.488, C:V.685 Hydrogen bonds: C:A.689, C:T.690, C:T.690, C:N.721, C:E.738 Salt bridges: C:R.523, C:K.762 KAI.45: 11 residues within 4Å: Chain D: E.440, Y.488, P.516, A.518, R.523, V.685, G.688, A.689, T.690, N.721, E.738 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.488, D:V.685 Hydrogen bonds: D:A.518, D:A.689, D:T.690, D:T.690, D:E.738 Salt bridges: D:R.523, D:K.762

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

POV.12: 17 residues within 4Å: Chain A: G.551, V.552, F.553, L.556, N.557, P.561, W.564, L.568, L.619, M.620, V.826 Chain D: G.638, I.639, F.642, L.645 Ligands: POV.13, POV.15 Ligand excluded by PLIP POV.13: 6 residues within 4Å: Chain A: F.553, L.568, F.612, A.829, L.833 Ligands: POV.12 Ligand excluded by PLIP POV.14: 8 residues within 4Å: Chain A: N.549, V.552, V.817, F.824, I.825, V.832 Chain D: Y.566, V.577 Ligand excluded by PLIP POV.15: 10 residues within 4Å: Chain A: L.572, L.609, L.833, Y.844, K.848 Chain D: Y.587 Chain E: I.366, V.370 Ligands: POV.12, POV.43 Ligand excluded by PLIP POV.21: 14 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, V.837, G.840, E.841, Y.844 Ligands: POV.26 Ligand excluded by PLIP POV.25: 22 residues within 4Å: Chain A: R.634, I.635, G.638, I.639, F.642, L.645 Chain B: G.551, V.552, F.553, L.556, P.561, W.564, L.568, F.612, W.613, V.616, L.619, M.620, I.647, I.648, V.826 Ligands: POV.26 Ligand excluded by PLIP POV.26: 13 residues within 4Å: Chain A: I.635, I.639 Chain B: F.553, L.568, F.612, I.825, V.826, A.829, G.830, L.833 Ligands: POV.21, POV.25, POV.27 Ligand excluded by PLIP POV.27: 14 residues within 4Å: Chain A: Y.566, G.573, V.577 Chain B: V.817, F.824, I.825, A.828, A.829, L.831, V.832, V.835 Chain E: T.354, L.361 Ligands: POV.26 Ligand excluded by PLIP POV.33: 8 residues within 4Å: Chain B: Y.566, V.577 Chain C: V.817, G.821, F.824, A.828, L.831, V.832 Ligand excluded by PLIP POV.35: 18 residues within 4Å: Chain B: R.634, G.638, I.639, F.642 Chain C: G.551, F.553, L.556, N.557, P.561, W.564, L.568, W.613, V.616, L.619, M.620, V.826 Ligands: POV.36, POV.44 Ligand excluded by PLIP POV.36: 8 residues within 4Å: Chain C: F.553, L.568, F.612, V.616, A.829, L.833 Ligands: POV.35, POV.44 Ligand excluded by PLIP POV.43: 9 residues within 4Å: Chain A: T.607, L.609, F.836, G.840, Y.844 Chain D: Y.587, L.631 Chain E: R.374 Ligands: POV.15 Ligand excluded by PLIP POV.44: 9 residues within 4Å: Chain B: Y.587, L.631 Chain C: L.609, G.840, Y.844 Chain D: Q.872, R.873 Ligands: POV.35, POV.36 Ligand excluded by PLIP POV.46: 20 residues within 4Å: Chain C: I.635, G.638, I.639, F.642, L.645 Chain D: G.551, F.553, L.556, P.561, W.564, L.568, F.612, W.613, V.616, L.619, M.620, I.647, I.648, V.826 Ligands: POV.47 Ligand excluded by PLIP POV.47: 11 residues within 4Å: Chain C: L.631, I.639 Chain D: F.553, L.568, F.612, V.616, V.826, A.829, L.833 Ligands: POV.46, POV.48 Ligand excluded by PLIP POV.48: 12 residues within 4Å: Chain C: Y.566, G.573 Chain D: V.817, Q.818, G.821, F.824, I.825, A.829, L.831, V.832, L.833 Ligands: POV.47 Ligand excluded by PLIP POV.49: 13 residues within 4Å: Chain A: K.870 Chain C: Y.587, L.631 Chain D: F.579, V.580, R.583, L.608, L.609, L.833, F.836, V.837, G.840, E.841 Ligand excluded by PLIP

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

NAG.16: 2 residues within 4Å: Chain A: N.67, T.69 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: P.72, N.73 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.275, L.394, K.395 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.412 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: C.750, N.751 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.67, T.69 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: P.72, N.73 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.412 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: R.543, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.5 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.67, T.69 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: T.33, N.73 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: G.273, N.275 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.412 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: C.750, N.751 Ligands: NAG-NAG-BMA-BMA.7 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.67, T.69 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: P.72, N.73 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain D: N.412 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain D: R.543, N.751 Ligands: NAG-NAG-BMA-BMA.10 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: A.184, S.300, N.311, S.313 Ligand excluded by PLIP

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

2J9.22: 13 residues within 4Å: Chain A: P.532, M.534, T.535, S.761, K.762, G.763 Chain D: K.531, P.532, F.533, L.783, Q.786, L.791 Ligands: 2J9.42 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Q.786, D:L.791, A:P.532 Halogen bonds: A:M.534 2J9.23: 14 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, L.783, Q.786, L.791 Chain C: P.532, M.534, T.535, S.761, K.762, G.763 Ligands: 2J9.32 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.786, B:L.791, C:P.532 Halogen bonds: C:M.534 2J9.32: 14 residues within 4Å: Chain B: I.519, P.532, T.535, S.761, K.762, G.763 Chain C: K.531, P.532, F.533, M.534, L.783, Q.786, L.791 Ligands: 2J9.23 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.786, C:L.791, B:P.532 2J9.42: 13 residues within 4Å: Chain A: K.531, P.532, F.533, T.535, L.783, Q.786, L.791 Chain D: P.532, T.535, S.761, K.762, G.763 Ligands: 2J9.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Q.786, A:L.791, D:P.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Activation of kainate receptor GluK2-Neto2 complex. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-09-17

Peptides

Glutamate receptor ionotropic, kainate 2: ABCD
Neuropilin and tolloid-like protein 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, kainate 2

Neuropilin and tolloid-like protein 2

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