SMTL ID : 5mfv.1

Crystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-521 at 2.18 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x 5PX: 4-Cyclopropyl-3,4-dihydro-7-hydroxy-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

5PX.1: 16 residues within 4Å: Chain A: K.103, P.104, F.105, M.106, T.107, L.235, Q.238, L.243 Chain B: I.91, P.104, M.106, T.107, S.213, K.214, G.215 Ligands: 5PX.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.104, A:L.243 Hydrogen bonds: B:T.107 5PX.2: 16 residues within 4Å: Chain A: I.91, P.104, M.106, T.107, S.213, K.214, G.215 Chain B: K.103, P.104, F.105, M.106, T.107, L.235, Q.238, L.243 Ligands: 5PX.1 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.243, A:P.104, A:T.107 Hydrogen bonds: A:T.107

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

KAI.3: 13 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, S.173, E.190, Y.216 14 PLIP interactions: 14 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:T.142, A:E.190 Water bridges: A:V.137, A:V.137, A:E.190, A:E.190 Salt bridges: A:R.95 KAI.7: 12 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, G.140, S.141, T.142, S.173, E.190, Y.216 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:T.90, B:S.141, B:T.142, B:T.142, B:E.190 Water bridges: B:V.137, B:M.143, B:E.190 Salt bridges: B:R.95

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

CL.4: 3 residues within 4Å: Chain A: K.103, R.227 Chain B: K.103 Ligand excluded by PLIP

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

SO4.5: 4 residues within 4Å: Chain A: Q.238, H.244 Chain B: D.212, S.213 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.212, B:S.213, A:Q.238, A:Q.238 Salt bridges: A:H.244 SO4.8: 4 residues within 4Å: Chain A: D.212, S.213 Chain B: Q.238, H.244 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.238, A:D.212, A:S.213, A:S.213 Salt bridges: B:H.244 SO4.9: 3 residues within 4Å: Chain B: R.31, K.54, L.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.55 Salt bridges: B:R.31

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.60, Y.61, V.137, R.138, D.139, G.140, K.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.61, A:R.138

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

ACT.10: 3 residues within 4Å: Chain B: R.20, S.22, K.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.24 Salt bridges: B:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsen, A.P. et al., Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors. Mol. Pharmacol. (2017)

Release Date

2017-04-12

Peptides

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1

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