SMTL ID : 9n4r.1

Composite map for GluK2-0xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

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: 7 residues within 4Å: Chain A: R.158, D.162, R.194, Y.195, N.378, N.381, T.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158 NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain B: R.158, D.162, N.378, N.381, T.385, P.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.194, B:R.158 NAG-NAG-BMA-MAN-MAN.5: 6 residues within 4Å: Chain C: R.158, D.162, Q.165, N.378, N.381, T.385 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.158 NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain D: R.158, D.162, R.194, N.378, N.381, T.385, P.407 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.194, D:R.158

2 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: 10 residues within 4Å: Chain B: F.167, G.273, V.274, N.275, S.393, K.395, E.397, Q.417, G.419, K.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.397, B:Q.417, B:K.420 NAG-NAG.6: 10 residues within 4Å: Chain D: F.167, G.273, V.274, N.275, S.393, K.395, E.397, Q.417, G.419, K.420 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.397, D:Q.417, D:K.420

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.4: 4 residues within 4Å: Chain B: R.543, N.546, T.730 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.8: 4 residues within 4Å: Chain D: R.543, N.546, T.730 Ligands: NAG.52 No protein-ligand interaction detected (PLIP)

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

KAI.9: 11 residues within 4Å: Chain A: E.440, Y.488, P.516, A.518, R.523, V.685, A.689, T.690, N.721, L.736, E.738 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.488, A:V.685, A:E.738 Hydrogen bonds: A:A.689, A:T.690, A:T.690, A:N.721 Salt bridges: A:R.523 KAI.24: 10 residues within 4Å: Chain B: E.440, Y.488, P.516, A.518, R.523, V.685, 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:N.721, B:E.738 Salt bridges: B:R.523 KAI.32: 11 residues within 4Å: Chain C: E.440, Y.488, P.516, A.518, R.523, V.685, A.689, T.690, N.721, L.736, E.738 7 PLIP interactions: 7 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 Salt bridges: C:R.523 KAI.44: 10 residues within 4Å: Chain D: E.440, Y.488, P.516, A.518, R.523, V.685, A.689, T.690, N.721, E.738 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.488, D:V.685, D:V.685 Hydrogen bonds: D:A.518, D:A.689, D:N.721, D:E.738 Salt bridges: D:R.523

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

POV.10: 16 residues within 4Å: Chain A: F.553, L.556, P.561, W.564, M.565, L.568, W.613, L.619, I.647, I.648 Chain D: G.638, I.639, F.642, L.645 Ligands: POV.11, POV.13 Ligand excluded by PLIP POV.11: 9 residues within 4Å: Chain A: F.553, L.568, L.572, F.612, V.616, A.829, L.833 Ligands: POV.10, POV.13 Ligand excluded by PLIP POV.12: 6 residues within 4Å: Chain A: V.552, V.817, Q.818, G.821, V.832 Chain D: Y.566 Ligand excluded by PLIP POV.13: 11 residues within 4Å: Chain A: T.607, L.609, F.612, L.833, F.836, G.840, E.841, Y.844 Chain D: Y.587 Ligands: POV.10, POV.11 Ligand excluded by PLIP POV.20: 13 residues within 4Å: Chain A: L.631, R.634, I.635, I.639 Chain B: L.568, L.609, F.612, W.613, V.616, A.829, L.833 Ligands: POV.21, POV.25 Ligand excluded by PLIP POV.21: 9 residues within 4Å: Chain A: Y.587 Chain B: L.608, L.609, F.612, L.833, F.836, V.837, G.840 Ligands: POV.20 Ligand excluded by PLIP POV.25: 17 residues within 4Å: Chain A: G.638, I.639, F.642, L.645 Chain B: G.551, F.553, S.554, L.556, N.557, P.561, W.564, L.568, L.619, M.620, I.647, V.826 Ligands: POV.20 Ligand excluded by PLIP POV.26: 11 residues within 4Å: Chain A: Y.566 Chain B: N.549, P.550, V.817, Q.818, G.821, F.824, I.825, A.829, L.831, V.832 Ligand excluded by PLIP POV.33: 17 residues within 4Å: Chain B: G.638, I.639, F.642, L.645 Chain C: F.553, L.556, P.561, W.564, M.565, L.568, W.613, V.616, L.619, I.647, I.648 Ligands: POV.34, POV.36 Ligand excluded by PLIP POV.34: 10 residues within 4Å: Chain C: F.553, P.561, L.568, L.572, F.612, V.616, A.829, L.833 Ligands: POV.33, POV.36 Ligand excluded by PLIP POV.35: 9 residues within 4Å: Chain B: Y.566, G.573 Chain C: V.552, V.817, Q.818, G.821, A.829, L.831, V.832 Ligand excluded by PLIP POV.36: 13 residues within 4Å: Chain B: Y.587, L.631 Chain C: T.607, L.608, L.609, F.612, L.833, F.836, V.837, E.841, Y.844 Ligands: POV.33, POV.34 Ligand excluded by PLIP POV.45: 17 residues within 4Å: Chain C: G.638, F.642, L.645 Chain D: G.551, F.553, S.554, L.556, N.557, P.561, W.564, L.568, L.619, M.620, I.647, I.648, V.826 Ligands: POV.46 Ligand excluded by PLIP POV.46: 12 residues within 4Å: Chain C: L.631, R.634, I.639 Chain D: L.568, L.609, F.612, W.613, V.616, A.829, L.833 Ligands: POV.45, POV.48 Ligand excluded by PLIP POV.47: 10 residues within 4Å: Chain D: N.549, P.550, V.817, Q.818, G.821, F.824, I.825, A.829, L.831, V.832 Ligand excluded by PLIP POV.48: 10 residues within 4Å: Chain C: Y.587 Chain D: L.608, L.609, F.612, L.833, F.836, V.837, G.840, Y.844 Ligands: POV.46 Ligand excluded by PLIP

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

NAG.14: 3 residues within 4Å: Chain A: N.67, R.68, T.69 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: P.72, N.73 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain A: E.250, Y.251, G.273, N.275, L.394, K.395 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.412 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.19 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: R.543, C.750, N.751 Ligands: NAG.18 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.67, T.69 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: P.72, N.73 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.412 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.4 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.67, R.68, T.69 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: P.72, N.73 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain C: E.250, Y.251, G.273, N.275, L.394, K.395 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: R.543, N.546 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: R.543, N.749, C.750, N.751 Ligands: NAG.41 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.67, T.69 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: P.72, N.73 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain D: N.412 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain D: N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.8 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: 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, T.535, L.783, Q.786, L.791 Ligands: 2J9.43 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:P.532, D:T.535, D:Q.786, D:L.791 Halogen bonds: A:M.534 2J9.23: 15 residues within 4Å: Chain B: K.531, P.532, F.533, 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: 2J9.31 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.535, B:Q.786, B:L.791, C:P.532 Halogen bonds: C:M.534 2J9.31: 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, L.783, Q.786, L.791 Ligands: 2J9.23 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.786, C:L.791, B:P.532 Halogen bonds: B:M.534 2J9.43: 14 residues within 4Å: Chain A: K.531, P.532, F.533, L.783, Q.786, L.791 Chain D: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Ligands: 2J9.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Q.786, A:L.791, D:P.532 Halogen bonds: D:M.534

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

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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