SMTL ID : 9n4o.1

Composite map for GluK2-0xNeto2 in the apo state with asymmetric 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: E.250, Y.251, Y.252, N.275, K.418 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: S.427, L.428, S.429, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: R.543, N.546, L.729, T.730 Ligands: NAG.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:T.730 NAG-NAG.6: 7 residues within 4Å: Chain B: E.250, G.273, N.275, S.393, L.394, K.395, I.402 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.393, B:L.394, B:K.395 NAG-NAG.8: 1 residues within 4Å: Chain B: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain B: N.423, I.424, D.426, L.428, N.430, R.431 Ligands: NAG.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.428, B:N.430 NAG-NAG.11: 6 residues within 4Å: Chain C: E.250, Y.251, Y.252, N.275, L.394, K.395 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.395 NAG-NAG.13: 1 residues within 4Å: Chain C: N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: F.167, G.273, N.275 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.167 NAG-NAG.16: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-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, T.385, W.405, P.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158, A:D.162

2 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.3: 2 residues within 4Å: Chain A: T.404, N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain D: S.154, S.155, R.158, N.378, N.381, T.385 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.155, D:R.158, D:R.158, D:R.158, D:R.158

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.7: 6 residues within 4Å: Chain B: R.158, D.162, N.378, T.380, T.385, S.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.158, B:R.158 NAG-NAG-BMA-MAN-MAN.12: 6 residues within 4Å: Chain C: R.158, D.162, R.194, N.378, T.380, T.385 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.10: 5 residues within 4Å: Chain B: R.543, N.546, L.729, T.730 Ligands: NAG.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.543, B:L.729

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

POV.17: 11 residues within 4Å: Chain A: F.553, L.556, N.557, P.561, W.564, V.567, M.620, V.826 Chain D: G.638, I.639, F.642 Ligand excluded by PLIP POV.18: 4 residues within 4Å: Chain A: V.817, Q.818, I.825 Chain D: Y.566 Ligand excluded by PLIP POV.23: 5 residues within 4Å: Chain A: Y.566, A.570 Chain B: V.817, F.824, I.825 Ligand excluded by PLIP POV.24: 9 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.608, L.609, F.612, G.840, E.841, Y.844 Ligands: POV.26 Ligand excluded by PLIP POV.25: 15 residues within 4Å: Chain A: R.634, I.639, F.642, L.645 Chain B: F.553, L.556, W.564, L.568, W.613, V.616, L.619, M.620, I.647, V.826 Ligands: POV.26 Ligand excluded by PLIP POV.26: 7 residues within 4Å: Chain A: I.635 Chain B: I.825, A.829, G.830, L.833 Ligands: POV.24, POV.25 Ligand excluded by PLIP POV.31: 7 residues within 4Å: Chain B: F.642 Chain C: F.553, L.556, W.564, L.568, M.620 Ligands: POV.32 Ligand excluded by PLIP POV.32: 8 residues within 4Å: Chain B: I.635 Chain C: F.612, I.825, V.826, A.829, L.833 Ligands: POV.31, POV.33 Ligand excluded by PLIP POV.33: 8 residues within 4Å: Chain B: Y.566 Chain C: V.817, Q.818, A.828, A.829, V.832, L.833 Ligands: POV.32 Ligand excluded by PLIP POV.34: 4 residues within 4Å: Chain B: L.631 Chain C: F.579, L.608, Y.844 Ligand excluded by PLIP POV.39: 9 residues within 4Å: Chain A: T.607, L.608, L.609, F.612, F.836, G.840, Y.844 Chain D: Y.587, K.629 Ligand excluded by PLIP POV.40: 13 residues within 4Å: Chain C: F.642 Chain D: F.553, L.556, W.564, V.567, L.568, L.619, M.620, I.647, I.648, Y.651 Ligands: POV.41, POV.43 Ligand excluded by PLIP POV.41: 8 residues within 4Å: Chain D: I.825, V.826, A.828, A.829, G.830, V.832 Ligands: POV.40, POV.43 Ligand excluded by PLIP POV.42: 8 residues within 4Å: Chain C: Y.566, G.573, C.576, V.577 Chain D: V.552, V.817, F.824, L.831 Ligand excluded by PLIP POV.43: 7 residues within 4Å: Chain C: L.631 Chain D: F.612, L.833, E.841, Y.844 Ligands: POV.40, POV.41 Ligand excluded by PLIP

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

NAG.19: 3 residues within 4Å: Chain A: N.67, T.69, L.70 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: P.72, N.73 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.422, N.423, I.424, T.425 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: R.543, L.729, N.749, N.751 Ligands: NAG-NAG.5, NAG-NAG.5 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: 3 residues within 4Å: Chain B: N.423, N.430 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: C.750, N.751 Ligands: NAG-NAG-BMA-BMA.10, NAG-NAG-BMA-BMA.10 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: P.72, N.73 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.412, E.415 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: T.425, N.430, S.432 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: R.543, N.749, N.751 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.67, T.69 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: P.72, N.73 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.546 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain D: L.729, N.749, C.750, N.751 Ligand excluded by 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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