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

Crystal structure of the kainate receptor GluK3-H523A ligand binding domain in complex with kainate at 2.7A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: K.62, Y.63, G.64, A.65, N.73, D.141 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.62, A:A.65, A:D.141 Hydrogen bonds: A:Y.63, A:G.64, A:N.73 ACT.9: 5 residues within 4Å: Chain A: L.211, I.212 Chain B: D.242, H.245 Ligands: ZN.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.245 ACT.10: 3 residues within 4Å: Chain B: Y.63, G.64, D.141 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.141 Hydrogen bonds: B:Y.63, B:G.64

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: D.242, H.245 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.242, A:D.242, A:H.245 ZN.3: 2 residues within 4Å: Chain A: H.82 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.82 ZN.11: 3 residues within 4Å: Chain B: D.242, H.245 Ligands: ACT.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.242, B:H.245

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

CL.4: 3 residues within 4Å: Chain A: F.103, K.105 Chain B: K.105 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: R.33, I.55, R.56, L.57 Ligands: GOL.16 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: R.22, S.24, R.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24 Salt bridges: A:R.22, A:R.26 SO4.6: 4 residues within 4Å: Chain A: R.33, I.55, R.56, L.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.57 Salt bridges: A:R.33 SO4.7: 2 residues within 4Å: Chain A: H.82 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.82 SO4.14: 3 residues within 4Å: Chain B: R.22, S.24, R.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.22, B:S.24, B:D.25, B:R.26 Salt bridges: B:R.26

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

KAI.8: 13 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, Y.217 9 PLIP interactions: 9 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:T.144, A:E.191 Salt bridges: A:R.97 KAI.15: 12 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 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:T.144, B:E.191 Salt bridges: B:R.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 3 residues within 4Å: Chain B: L.57, E.59 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.59, B:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bay, Y. et al., Small-molecule positive allosteric modulation of homomeric kainate receptors GluK1-3: development of screening assays and insight into GluK3 structure. Febs J. (2024)

Release Date

2023-12-13

Peptides

Glutamate receptor ionotropic, kainate 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Glutamate receptor ionotropic, kainate 3

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