SMTL ID : 8r36.1

Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

KAI.1: 11 residues within 4Å: Chain A: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, E.190 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.61, A:V.137 Hydrogen bonds: A:P.88, A:T.90, A:T.90, A:S.141, A:T.142, A:E.190 Water bridges: A:V.137, A:M.143, A:E.190 Salt bridges: A:R.95 KAI.14: 11 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, E.190 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.61, B:V.137 Hydrogen bonds: B:T.90, B:S.141, B:T.142, B:T.142, B:E.190 Water bridges: B:V.137, B:V.137, B:E.190 Salt bridges: B:R.95

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

SO4.2: 2 residues within 4Å: Chain A: R.4, Y.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.226, A:Y.226 Salt bridges: A:R.4 SO4.15: 1 residues within 4Å: Chain B: R.164 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.164, B:R.179, B:R.179 Salt bridges: B:R.164 SO4.16: 5 residues within 4Å: Chain B: R.20, S.22, D.23, K.24, L.26 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.20, B:K.24 SO4.17: 2 residues within 4Å: Chain B: R.31, K.54 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.31, B:R.31, B:R.31 Salt bridges: B:R.31, B:K.54

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

CL.3: 2 residues within 4Å: Chain A: L.50, Y.51 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.103 Chain B: K.103 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: G.209, L.210 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.69, W.70, K.75 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: T.130 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: G.117 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: L.50, Y.51 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: K.150, I.151, S.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.152 GOL.10: 7 residues within 4Å: Chain A: E.14, S.173, D.174, I.177, M.189, S.193, Y.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.14, A:S.173, A:D.174, A:S.193 Water bridges: A:E.14, A:S.173, A:S.193 GOL.11: 8 residues within 4Å: Chain A: I.91, P.104, K.214, G.215 Chain B: K.103, P.104, L.235 Ligands: 9TE.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.91, A:G.215, B:P.104 GOL.12: 3 residues within 4Å: Chain A: K.147, W.158, S.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.147, A:S.162, A:S.162

1 x 9TE: 4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

9TE.13: 20 residues within 4Å: Chain A: K.103, P.104, F.105, M.106, T.107, S.213, K.214, L.235, Q.238, L.243 Chain B: I.91, P.104, F.105, M.106, T.107, S.213, K.214, G.215, Q.238 Ligands: GOL.11 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.107, A:Q.238, A:L.243, B:P.104 Hydrogen bonds: A:S.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bay, Y. et al., Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538. J.Struct.Biol. (2024)

Release Date

2024-08-14

Peptides

Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, kainate 1

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