SMTL ID : 9n4m.1

Composite map for GluK2 in the apo state with 2-fold symmetrical ligand-binding domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

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: 5 residues within 4Å: Chain A: D.152, R.158, N.378, N.381, T.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158 NAG-NAG.2: 2 residues within 4Å: Chain A: S.409, N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain B: F.167, G.273, N.275, L.394, K.395, E.396, G.419, K.420, P.421 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.396 Hydrogen bonds: B:E.396, B:E.396, B:G.419 NAG-NAG.5: 4 residues within 4Å: Chain B: R.543, N.546, T.730 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: R.543, L.729, N.749, C.750, N.751 Ligands: NAG-NAG.5, NAG-NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.729 NAG-NAG.7: 5 residues within 4Å: Chain C: D.152, R.158, N.378, N.381, T.385 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.158 NAG-NAG.8: 2 residues within 4Å: Chain C: S.409, N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 11 residues within 4Å: Chain D: F.167, G.273, V.274, N.275, S.393, L.394, K.395, E.396, G.419, K.420, P.421 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:E.396 Hydrogen bonds: D:E.396, D:E.396, D:G.419 NAG-NAG.11: 4 residues within 4Å: Chain D: R.543, N.546, T.730 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain D: R.543, L.729, N.749, C.750, N.751 Ligands: NAG-NAG.11, NAG-NAG.11 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.729

2 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.4: 8 residues within 4Å: Chain B: R.158, D.162, N.378, N.381, T.385, W.405, P.407, G.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 8 residues within 4Å: Chain D: R.158, D.162, N.378, N.381, T.385, W.405, P.407, G.410 No protein-ligand interaction detected (PLIP)

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

POV.13: 19 residues within 4Å: Chain A: P.550, F.553, L.556, P.561, W.564, V.567, L.568, F.612, W.613, V.616, L.619, M.620, I.648, V.826 Chain D: R.634, G.638, I.639, F.642 Ligands: POV.14 Ligand excluded by PLIP POV.14: 14 residues within 4Å: Chain A: F.553, L.568, C.571, L.572, F.612, V.616, V.826, A.829, G.830, L.833 Chain D: I.635, I.639 Ligands: POV.13, POV.40 Ligand excluded by PLIP POV.15: 7 residues within 4Å: Chain A: L.609, F.836, G.840, E.841, Y.844 Chain D: Y.587, L.631 Ligand excluded by PLIP POV.20: 11 residues within 4Å: Chain A: Y.566, L.569, G.573, V.577 Chain B: V.552, V.817, I.825, A.828, A.829, L.831 Ligands: POV.27 Ligand excluded by PLIP POV.21: 12 residues within 4Å: Chain A: Y.587, K.629, L.631 Chain B: T.607, L.608, L.609, N.610, L.833, F.836, V.837, G.840, E.841 Ligand excluded by PLIP POV.26: 18 residues within 4Å: Chain A: R.634, G.638, I.639, F.642, L.645 Chain B: P.550, F.553, L.556, P.561, W.564, V.567, L.568, V.616, L.619, M.620, I.648, V.826 Ligands: POV.27 Ligand excluded by PLIP POV.27: 11 residues within 4Å: Chain A: I.635, I.639 Chain B: V.552, F.553, L.568, L.572, V.826, A.829, L.833 Ligands: POV.20, POV.26 Ligand excluded by PLIP POV.31: 10 residues within 4Å: Chain B: Y.566, A.570 Chain C: F.824, I.825, A.829, L.831, V.832, L.833, V.835 Ligands: POV.34 Ligand excluded by PLIP POV.32: 8 residues within 4Å: Chain B: Y.587, L.631 Chain C: L.608, L.609, F.836, G.840, E.841, Y.844 Ligand excluded by PLIP POV.33: 19 residues within 4Å: Chain B: R.634, G.638, I.639, F.642 Chain C: P.550, F.553, L.556, P.561, W.564, V.567, L.568, F.612, W.613, V.616, L.619, M.620, I.648, V.826 Ligands: POV.34 Ligand excluded by PLIP POV.34: 14 residues within 4Å: Chain B: I.635, I.639 Chain C: F.553, L.568, C.571, L.572, F.612, V.616, V.826, A.829, G.830, L.833 Ligands: POV.31, POV.33 Ligand excluded by PLIP POV.39: 11 residues within 4Å: Chain C: Y.566, G.573, V.577 Chain D: V.552, V.817, F.824, I.825, A.828, A.829, L.831 Ligands: POV.42 Ligand excluded by PLIP POV.40: 8 residues within 4Å: Chain A: F.824, I.825, A.829, L.831, L.833 Chain D: Y.566, A.570 Ligands: POV.14 Ligand excluded by PLIP POV.41: 17 residues within 4Å: Chain C: R.634, G.638, I.639, F.642, L.645 Chain D: P.550, F.553, L.556, P.561, W.564, L.568, V.616, L.619, M.620, I.648, V.826 Ligands: POV.42 Ligand excluded by PLIP POV.42: 10 residues within 4Å: Chain C: I.639 Chain D: V.552, F.553, L.568, L.572, V.826, A.829, L.833 Ligands: POV.39, POV.41 Ligand excluded by PLIP POV.43: 13 residues within 4Å: Chain C: Y.587, K.629, L.631 Chain D: T.607, L.608, L.609, N.610, L.833, F.836, V.837, G.840, E.841, Y.844 Ligand excluded by PLIP

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

NAG.16: 2 residues within 4Å: Chain A: N.67, K.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.295 NAG.17: 3 residues within 4Å: Chain A: E.250, G.273, N.275 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.250 NAG.18: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.543 NAG.19: 4 residues within 4Å: Chain A: R.543, N.749, N.751 Ligands: NAG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:N.751 NAG.28: 3 residues within 4Å: Chain B: N.67, T.69, L.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.67 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.412 No protein-ligand interaction detected (PLIP) NAG.35: 2 residues within 4Å: Chain C: N.67, K.295 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.295 NAG.36: 3 residues within 4Å: Chain C: E.250, G.273, N.275 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.250 NAG.37: 3 residues within 4Å: Chain C: R.543, N.546 Ligands: NAG.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.543 NAG.38: 4 residues within 4Å: Chain C: R.543, N.749, N.751 Ligands: NAG.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.543, C:N.751 NAG.44: 3 residues within 4Å: Chain D: N.67, T.69, L.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.67 NAG.45: 2 residues within 4Å: Chain D: P.72, N.73 No protein-ligand interaction detected (PLIP) NAG.46: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.22: 4 residues within 4Å: Chain A: A.656 Chain B: A.656 Chain C: A.656 Chain D: A.656 No protein-ligand interaction detected (PLIP) NA.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.24: 4 residues within 4Å: Chain A: Q.621 Chain B: Q.621 Chain C: Q.621 Chain D: Q.621 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.621 NA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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