SMTL ID : 8r32.2 (1 other biounit)

Crystal structure of the GluK2 ligand-binding domain in complex with L-glutamate and BPAM344 at 1.60 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID

GLU.1: 14 residues within 4Å: Chain A: Y.61, P.89, L.90, A.91, R.96, V.138, G.141, A.142, T.143, M.144, N.174, M.190, E.191, Y.217 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:P.89, A:A.91, A:A.142, A:T.143, A:T.143, E.1, E.1 Water bridges: A:V.138, A:V.138, A:E.191 Salt bridges: A:R.96 GLU.7: 14 residues within 4Å: Chain B: Y.61, P.89, L.90, A.91, R.96, V.138, G.141, A.142, T.143, M.144, N.174, M.190, E.191, Y.217 12 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:P.89, B:A.91, B:A.142, B:T.143, B:T.143, E.7, E.7 Water bridges: B:V.138, B:V.138, B:E.191 Salt bridges: B:R.96

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

2J9.2: 17 residues within 4Å: Chain A: I.92, P.105, M.107, T.108, S.214, K.215, G.216 Chain B: K.104, P.105, F.106, M.107, T.108, I.235, L.236, Q.239, L.244 Ligands: 2J9.8 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.105, B:T.108, B:Q.239, B:L.244 Hydrogen bonds: A:G.216, B:P.105 Halogen bonds: A:M.107 2J9.8: 17 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, T.108, I.235, L.236, Q.239, L.244 Chain B: I.92, P.105, M.107, T.108, S.214, K.215, G.216 Ligands: 2J9.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.108, A:Q.239, A:L.244, B:P.105 Hydrogen bonds: A:P.105, B:G.216 Halogen bonds: B:M.107

4 x CL: CHLORIDE ION

CL.3: 5 residues within 4Å: Chain A: K.104, R.228 Chain B: K.104, R.228 Ligands: CL.9 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.31, F.32, R.54, L.55 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.104, R.228 Chain B: K.104, R.228 Ligands: CL.3 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.31, F.32, R.54, L.55 Ligand excluded by PLIP

4 x NA: SODIUM ION

NA.5: 4 residues within 4Å: Chain A: E.97, I.100, D.101, M.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.101, A:D.101 Water bridges: A:R.228 NA.6: 5 residues within 4Å: Chain A: I.46, I.233, A.234, Q.237 Chain B: Y.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.233 NA.11: 4 residues within 4Å: Chain B: E.97, I.100, D.101, M.223 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.97, B:D.101 Water bridges: B:R.228 NA.12: 5 residues within 4Å: Chain A: Y.94 Chain B: I.46, I.233, A.234, Q.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bay, Y. et al., The positive allosteric modulator BPAM344 and L-glutamate introduce an active-like structure of the ligand-binding domain of GluK2. Febs Lett. (2024)

Release Date

2024-09-18

Peptides

Glutamate receptor ionotropic, kainate 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Glutamate receptor ionotropic, kainate 2

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