SMTL ID : 9n4q.1

Composite map for GluK2-2xNeto2 in the apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

10 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: Y.251, H.253, N.275, E.415 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.67, T.69, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: G.273, N.275, K.395, K.418, G.419 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.420 NAG-NAG.7: 1 residues within 4Å: Chain B: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: R.543, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: R.543, N.546, L.729, T.730 Chain E: H.330 Ligands: NAG.37 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:T.730, E:H.330 NAG-NAG.13: 5 residues within 4Å: Chain D: N.275, L.394, K.395, K.420, P.421 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: R.543, N.751 Ligands: NAG-NAG-BMA-BMA.16 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: R.158, D.162, N.378, N.381, T.385, P.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.158, A:R.158, A:R.158 NAG-NAG-BMA-MAN-MAN.6: 6 residues within 4Å: Chain B: R.158, D.162, N.378, N.381, T.385 Chain F: K.125 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:R.158, B:R.158, F:K.125 NAG-NAG-BMA-MAN-MAN.11: 6 residues within 4Å: Chain C: R.158, D.162, N.378, N.381, T.385, P.407 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 10 residues within 4Å: Chain D: R.158, D.162, N.378, N.381, T.385, W.405, P.407, A.408, G.410 Chain E: K.125 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:R.158, E:K.125, E:K.125

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.8: 5 residues within 4Å: Chain B: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.16: 6 residues within 4Å: Chain D: R.543, N.546, T.548, T.730, S.731 Ligands: NAG-NAG.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.730

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.10: 4 residues within 4Å: Chain C: N.67, T.69, L.70, Q.288 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.288, C:Q.288

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

POV.18: 18 residues within 4Å: Chain A: P.550, G.551, F.553, L.556, P.561, W.564, M.565, L.568, C.571, L.572, F.612, V.616, L.619, M.620, V.826 Chain D: F.642, L.645 Ligands: POV.19 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.553, A:P.561, A:W.564, A:W.564, A:W.564, A:L.568, A:L.572, A:F.612, A:V.616, A:L.619, A:V.826, D:F.642, D:F.642, D:F.642, D:L.645 POV.19: 12 residues within 4Å: Chain A: V.552, F.553, L.568, L.609, W.613, V.826, A.829 Chain D: R.634, I.639 Ligands: POV.18, POV.20, POV.39 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.568, A:L.609, A:W.613, A:V.826, A:A.829, D:I.639 POV.20: 8 residues within 4Å: Chain A: V.552, I.825, L.831, V.832, L.833 Chain D: Y.566, V.577 Ligands: POV.19 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.566, D:Y.566, D:V.577, A:L.831, A:V.832, A:L.833 POV.26: 9 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.572, L.609, F.612, F.836, G.840, E.841, Y.844 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.572, B:L.609, B:F.836, B:E.841 Hydrogen bonds: A:Y.587 POV.27: 14 residues within 4Å: Chain A: I.639, F.642, L.645 Chain B: F.553, L.556, N.557, W.564, L.568, C.571, M.620, I.648, Y.651, V.826 Ligands: POV.28 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:I.639, A:F.642, A:F.642, A:F.642, A:L.645, B:F.553, B:L.556, B:W.564, B:W.564, B:L.568, B:L.568, B:I.648, B:Y.651, B:V.826 POV.28: 6 residues within 4Å: Chain A: R.634, G.638, I.639 Chain B: F.553, L.833 Ligands: POV.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.833 POV.31: 9 residues within 4Å: Chain B: F.642 Chain C: G.551, F.553, W.564, L.568, L.572, M.620, I.647 Ligands: POV.32 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.564, C:W.564, C:L.568, C:L.568, C:L.572, C:I.647, B:F.642 POV.32: 11 residues within 4Å: Chain B: I.639 Chain C: V.552, F.553, L.568, C.571, V.616, I.825, A.829, L.833 Ligands: POV.31, POV.33 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.568, C:V.616, C:A.829, C:L.833 POV.33: 8 residues within 4Å: Chain B: Y.566, G.573, V.577 Chain C: V.552, F.824, A.829, V.832 Ligands: POV.32 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.566, B:Y.566, B:Y.566, C:V.832 POV.38: 13 residues within 4Å: Chain A: Q.872 Chain C: Y.587, L.631 Chain D: L.572, L.608, L.609, F.612, V.616, L.833, V.837, E.841 Ligands: POV.40, POV.41 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.572, D:L.608, D:L.609, D:F.612, D:F.612, D:V.616, D:L.833, D:E.841 Hydrogen bonds: C:Y.587 POV.39: 5 residues within 4Å: Chain A: L.609 Chain D: Y.587, L.631 Chain F: I.366 Ligands: POV.19 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: D:L.631, F:I.366, A:L.609 POV.40: 17 residues within 4Å: Chain C: I.639, F.642, L.645, I.646 Chain D: F.553, L.556, N.557, W.564, L.568, V.616, L.619, M.620, I.647, Y.651, V.826 Ligands: POV.38, POV.41 16 PLIP interactions: 10 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.553, D:W.564, D:W.564, D:W.564, D:L.568, D:V.616, D:L.619, D:I.647, D:Y.651, D:V.826, C:F.642, C:F.642, C:F.642, C:F.642, C:L.645, C:I.646 POV.41: 11 residues within 4Å: Chain C: L.631, I.639 Chain D: F.553, W.613, V.616, A.829, G.830, L.833 Ligands: POV.38, POV.40, POV.42 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.631, C:I.639, D:W.613, D:V.616, D:A.829, D:L.833 POV.42: 7 residues within 4Å: Chain C: A.570 Chain D: V.817, F.824, I.825 Chain E: I.350, I.357 Ligands: POV.41 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: D:F.824, D:I.825, E:I.350, E:I.357, C:A.570 POV.46: 7 residues within 4Å: Chain B: V.817, F.824, A.828, V.832 Chain F: I.350, T.354, I.357 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:F.824, B:F.824, B:A.828, B:V.832, B:V.832, F:I.357

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

NAG.21: 3 residues within 4Å: Chain A: N.67, Q.288, W.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.67 NAG.22: 2 residues within 4Å: Chain A: P.72, N.73 No protein-ligand interaction detected (PLIP) NAG.23: 4 residues within 4Å: Chain A: D.426, S.427, N.430, R.431 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.430 Hydrogen bonds: A:S.427, A:R.431 NAG.24: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.543 NAG.25: 5 residues within 4Å: Chain A: R.543, L.729, N.749, N.751 Ligands: NAG.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.543, A:R.543, A:L.729 NAG.29: 2 residues within 4Å: Chain B: P.72, N.73 No protein-ligand interaction detected (PLIP) NAG.30: 1 residues within 4Å: Chain B: N.430 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.430 NAG.34: 1 residues within 4Å: Chain C: N.73 No protein-ligand interaction detected (PLIP) NAG.35: 2 residues within 4Å: Chain C: F.167, N.275 No protein-ligand interaction detected (PLIP) NAG.36: 1 residues within 4Å: Chain C: N.412 No protein-ligand interaction detected (PLIP) NAG.37: 4 residues within 4Å: Chain C: R.543, L.729, N.751 Ligands: NAG-NAG.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.543, C:R.543, C:L.729 NAG.43: 2 residues within 4Å: Chain D: N.67, Q.288 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.67 NAG.44: 1 residues within 4Å: Chain D: N.73 No protein-ligand interaction detected (PLIP) NAG.45: 3 residues within 4Å: Chain E: S.300, N.311, S.313 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.300, E:S.300, E:S.313, E:S.313 NAG.47: 3 residues within 4Å: Chain F: S.300, N.311, S.313 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.313

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: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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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