SMTL ID : 8fwq.1

Structure of kainate receptor GluK2 in complex with the positive allosteric modulator BPAM344

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 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: 2 residues within 4Å: Chain A: R.543, N.751 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: Y.271, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: R.543, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: D.426, S.427, S.429, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: R.543, N.751 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: Y.271, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain D: R.543, N.749, C.750, N.751 Ligands: NAG-NAG-BMA-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain D: D.426, S.427, S.429, N.430 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: R.158, N.378, T.380, T.385 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain C: R.158, F.377, N.378, T.380, T.385 No protein-ligand interaction detected (PLIP)

6 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.4: 4 residues within 4Å: Chain A: N.67, T.69, L.70, Q.288 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.69 NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: F.377, N.378, T.380, T.385 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.158 NAG-NAG-BMA.9: 3 residues within 4Å: Chain B: N.67, L.70, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: N.67, T.69, L.70, Q.288 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.69 NAG-NAG-BMA.16: 4 residues within 4Å: Chain D: F.377, N.378, T.380, T.385 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.158 NAG-NAG-BMA.18: 3 residues within 4Å: Chain D: N.67, L.70, Q.288 No protein-ligand interaction detected (PLIP)

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.5: 6 residues within 4Å: Chain B: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.14: 6 residues within 4Å: Chain D: R.543, N.546, T.548, T.730 Ligands: NAG-NAG.15, NAG-NAG.15 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: G.273, V.274, N.275 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain A: N.546 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain A: N.423, T.425 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG.25: 5 residues within 4Å: Chain B: H.225, H.253, V.274, N.275, K.395 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.275 Hydrogen bonds: B:H.225, B:H.253, B:K.395 NAG.26: 5 residues within 4Å: Chain B: K.418, K.420, N.423, I.424, T.425 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.425 Hydrogen bonds: B:K.418, B:K.418 NAG.27: 1 residues within 4Å: Chain B: N.412 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.412 NAG.30: 3 residues within 4Å: Chain C: G.273, V.274, N.275 No protein-ligand interaction detected (PLIP) NAG.31: 1 residues within 4Å: Chain C: N.546 No protein-ligand interaction detected (PLIP) NAG.32: 2 residues within 4Å: Chain C: N.423, T.425 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain C: N.412 No protein-ligand interaction detected (PLIP) NAG.35: 5 residues within 4Å: Chain D: H.225, H.253, V.274, N.275, K.395 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.275 Hydrogen bonds: D:H.225, D:H.253, D:K.395 NAG.36: 5 residues within 4Å: Chain D: K.418, K.420, N.423, I.424, T.425 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.425 Hydrogen bonds: D:K.418, D:K.418 NAG.37: 1 residues within 4Å: Chain D: N.412 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.412

4 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.23: 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, M.534, T.535, L.783, Q.786, L.791 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.535, D:Q.786, D:L.791, A:P.532 Halogen bonds: A:M.534 2J9.28: 15 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, M.534, T.535, L.783, Q.786, L.791 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.532, C:T.535, C:L.791 Halogen bonds: B:M.534 2J9.29: 15 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 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 2J9.34: 15 residues within 4Å: Chain A: K.531, P.532, F.533, M.534, T.535, L.783, Q.786, L.791 Chain D: I.519, P.532, M.534, T.535, S.761, K.762, G.763 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.532, A:T.535, A:L.791 Halogen bonds: D:M.534

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

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 A Hydrogen bonds: A:Q.621

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Positive and negative allosteric modulation of GluK2 kainate receptors by BPAM344 and antiepileptic perampanel. Cell Rep (2023)

Release Date

2023-04-19

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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