SMTL ID : 9n4p.1

Composite map for GluK2-1xNeto2 in the apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

5 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, N.378, T.380, N.381, T.385, P.407 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain A: R.543, N.546, V.728, L.729, T.730, S.731, D.732 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.729 NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain B: R.158, D.162, R.194, Y.195, N.378, T.385, W.405, P.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.194, B:R.194, B:R.158 NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain C: R.158, D.162, Y.195, N.378, T.385 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 6 residues within 4Å: Chain D: R.158, D.162, N.378, N.381, T.385, P.407 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.158

11 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: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: R.543, N.751 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.67, T.69, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: G.273, N.275, L.394, K.395, K.418 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.418, B:K.418 NAG-NAG.8: 1 residues within 4Å: Chain B: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: R.543, N.749, N.751 Ligands: NAG-NAG-BMA-BMA.9, NAG-NAG-BMA-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: R.66, N.67, T.69, L.70, W.368 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: R.543, N.546 Chain E: H.330 Ligands: NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: E.250, N.275, K.395 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain D: R.543, N.546, T.730 Ligands: NAG.45 No protein-ligand interaction detected (PLIP)

1 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.9: 7 residues within 4Å: Chain B: R.543, N.546, T.548, T.730, D.732 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP)

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

POV.18: 17 residues within 4Å: Chain A: P.550, G.551, F.553, L.556, P.561, W.564, M.565, L.568, F.612, V.616, L.619, M.620, I.648, V.826 Chain D: F.642, L.645 Ligands: POV.19 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain A Hydrophobic interactions: D:F.642, D:L.645, A:L.556, A:P.561, A:W.564, A:W.564, A:L.568, A:L.568, A:F.612, A:V.616, A:L.619, A:I.648, A:V.826, A:V.826 POV.19: 12 residues within 4Å: Chain A: F.553, L.568, F.612, W.613, V.616, I.825, V.826, A.829 Chain D: G.638, I.639 Ligands: POV.18, POV.20 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.568, A:F.612, A:W.613, A:W.613, A:V.616, A:V.616, D:I.639 POV.20: 8 residues within 4Å: Chain A: F.824, I.825, A.828, A.829, L.831 Chain D: A.570, V.577 Ligands: POV.19 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.824, A:I.825, A:A.828, A:A.829, A:L.831, D:A.570 POV.21: 6 residues within 4Å: Chain A: L.609, F.612, G.840, E.841, Y.844 Chain D: Y.587 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.609, A:F.612, A:F.612, A:Y.844, A:Y.844, A:Y.844 POV.26: 9 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.608, F.612, G.840, E.841, Y.844 Chain C: Q.872, R.873 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.608, B:F.612, B:E.841, B:Y.844, B:Y.844 Hydrogen bonds: A:Y.587 POV.27: 15 residues within 4Å: Chain A: F.642, L.645 Chain B: F.553, L.556, W.564, V.567, L.568, L.572, F.612, V.616, L.619, M.620, I.647, V.826 Ligands: POV.28 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.553, B:L.556, B:L.556, B:W.564, B:W.564, B:W.564, B:V.567, B:L.568, B:L.572, B:F.612, B:V.616, B:L.619, B:I.647, B:V.826, A:F.642, A:F.642, A:L.645 POV.28: 11 residues within 4Å: Chain A: I.635, I.639 Chain B: V.552, F.553, F.612, W.613, V.616, A.829, G.830, L.833 Ligands: POV.27 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.612, B:W.613, B:W.613, B:V.616, B:A.829, A:I.635, A:I.639 POV.29: 6 residues within 4Å: Chain A: Y.566, G.573 Chain B: V.817, F.824, A.829, L.831 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.824, B:L.831 POV.32: 4 residues within 4Å: Chain B: Y.566 Chain C: N.549, I.825 Ligands: POV.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.825 POV.33: 14 residues within 4Å: Chain B: F.642, L.645 Chain C: P.550, G.551, L.556, P.561, W.564, M.565, V.567, L.568, L.619, M.620 Chain E: L.339 Ligands: POV.34 9 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E, 5 interactions with chain C Hydrophobic interactions: B:F.642, B:L.645, E:L.339, E:L.339, C:W.564, C:W.564, C:V.567, C:L.568, C:L.619 POV.34: 7 residues within 4Å: Chain C: F.553, L.568, F.612, V.616, L.833 Ligands: POV.32, POV.33 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.553, C:L.568, C:L.568, C:F.612, C:V.616, C:L.833 POV.39: 15 residues within 4Å: Chain C: G.638, I.639, F.642, L.645 Chain D: F.553, L.556, W.564, M.565, V.567, L.568, L.619, M.620, I.647, I.648 Ligands: POV.40 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.553, D:L.556, D:L.556, D:W.564, D:W.564, D:V.567, D:L.568, D:L.568, D:I.647, D:I.648, C:I.639, C:F.642, C:L.645 POV.40: 12 residues within 4Å: Chain C: I.635, G.638, I.639 Chain D: F.612, W.613, V.616, A.829, G.830, L.833 Ligands: POV.39, POV.41, POV.42 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.612, D:W.613, D:W.613, D:V.616, D:V.616, D:A.829, C:I.635, C:I.639 POV.41: 8 residues within 4Å: Chain D: F.824, I.825, A.828, A.829, V.832 Chain E: T.354, I.357 Ligands: POV.40 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.824, D:I.825, D:A.828, D:A.829, D:V.832, D:V.832, E:I.357 POV.42: 8 residues within 4Å: Chain A: Q.872 Chain C: Y.587, L.631 Chain D: F.836, G.840, Y.844, K.848 Ligands: POV.40 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.836, C:Y.587, C:L.631 Hydrogen bonds: D:Y.844, D:Y.844

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

NAG.22: 1 residues within 4Å: Chain A: N.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.67 NAG.23: 1 residues within 4Å: Chain A: N.73 No protein-ligand interaction detected (PLIP) NAG.24: 4 residues within 4Å: Chain A: F.167, E.250, H.253, N.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.275 NAG.25: 4 residues within 4Å: Chain A: D.426, S.427, N.430, R.431 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain B: P.72, N.73 No protein-ligand interaction detected (PLIP) NAG.31: 1 residues within 4Å: Chain B: N.430 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.430 NAG.35: 1 residues within 4Å: Chain C: N.73 No protein-ligand interaction detected (PLIP) NAG.36: 5 residues within 4Å: Chain C: F.167, E.250, Y.252, H.253, N.275 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.167 Hydrogen bonds: C:N.275 NAG.37: 2 residues within 4Å: Chain C: T.404, N.412 No protein-ligand interaction detected (PLIP) NAG.38: 4 residues within 4Å: Chain C: R.543, N.749, N.751 Ligands: NAG-NAG.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.543, C:R.543 NAG.43: 1 residues within 4Å: Chain D: N.67 No protein-ligand interaction detected (PLIP) NAG.44: 2 residues within 4Å: Chain D: P.72, N.73 No protein-ligand interaction detected (PLIP) NAG.45: 5 residues within 4Å: Chain D: R.543, N.546, N.749, N.751 Ligands: NAG-NAG.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.543, D:N.546, D:N.751 NAG.46: 4 residues within 4Å: Chain E: S.300, N.311, N.312, S.313 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.300, E:S.300, E:N.312, E:S.313, E: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: 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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