SMTL ID : 8bsu.4 (3 other biounits)

Crystal structure of the kainate receptor GluK3-H523A ligand binding domain in complex with kainate and the positive allosteric modulator BPAM344 at 2.9A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

2J9.1: 15 residues within 4Å: Chain A: K.105, P.106, F.107, M.108, T.109, L.236, Q.239 Chain B: I.93, P.106, M.108, T.109, S.214, K.215, G.216 Ligands: 2J9.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.106, A:T.109, A:Q.239 Halogen bonds: B:M.108 2J9.10: 16 residues within 4Å: Chain A: I.93, P.106, M.108, T.109, S.214, K.215, G.216 Chain B: K.105, P.106, F.107, M.108, T.109, L.236, Q.239 Ligands: 2J9.1, CL.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.109, B:Q.239, A:P.106 Halogen bonds: A:M.108

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.242, H.245 Chain B: I.212 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.242 ZN.3: 3 residues within 4Å: Chain A: H.245, E.249 Ligands: ACT.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.245, A:E.249 ZN.11: 2 residues within 4Å: Chain B: H.245, E.249 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.245, B:E.249 ZN.12: 2 residues within 4Å: Chain B: D.242, H.245 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.242, B:D.242, B:H.245

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: N.202 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: K.105 Chain B: F.103, K.105, R.228 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: K.62, Y.63, D.141 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: M.108, T.109 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: K.62, Y.63, G.64, D.141 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: R.33, R.56, L.57 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: M.108, T.109 Ligands: 2J9.10 Ligand excluded by PLIP

2 x KAI: 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE(Non-covalent)

KAI.8: 12 residues within 4Å: Chain A: E.15, Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.63, A:V.139 Hydrogen bonds: A:T.92, A:T.92, A:A.143, A:T.144, A:E.191, A:E.191 Water bridges: A:V.139 Salt bridges: A:R.97 KAI.17: 13 residues within 4Å: Chain B: E.15, Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191, Y.217 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.63, B:V.139 Hydrogen bonds: B:P.90, B:T.92, B:A.143, B:T.144, B:E.191, B:E.191 Salt bridges: B:R.97

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain A: H.245, E.249 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.245

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.16: 3 residues within 4Å: Chain B: R.22, S.24, R.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.24, B:S.24 Salt bridges: B:R.22, B:R.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bay, Y. et al., Positive allosteric modulation of homomeric kainate receptors GluK1-3. To Be Published

Release Date

2023-12-13

Peptides

Glutamate receptor ionotropic, kainate 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

Glutamate receptor ionotropic, kainate 3

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