SMTL ID : 3c36.1

Crystal structure of GluR5 ligand-binding core in complex with ammonium ions at 1.68 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 3 residues within 4Å: Chain A: E.96, I.99, D.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100 Water bridges: A:R.227 NH4.7: 3 residues within 4Å: Chain B: E.96, I.99, D.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.100, B:D.100

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

CL.2: 4 residues within 4Å: Chain A: K.103, R.227 Chain B: K.103, R.227 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: R.31, K.54, L.55 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.31, K.54, L.55 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.20, S.22 Ligand excluded by PLIP

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

KAI.4: 12 residues within 4Å: Chain A: E.13, Y.61, P.88, L.89, T.90, R.95, G.140, S.141, T.142, E.190, Y.216 Ligands: GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:T.90, A:T.90, A:S.141, A:T.142, A:T.142, A:E.190 Water bridges: A:V.137, A:M.143, A:E.190 Salt bridges: A:R.95 KAI.10: 11 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, G.140, S.141, T.142, E.190 Ligands: GOL.11 11 PLIP interactions: 11 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, B:E.190 Salt bridges: B:R.95

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, G.140, K.171 Ligands: KAI.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:G.62, A:K.171 Water bridges: A:G.59, A:N.71 GOL.6: 9 residues within 4Å: Chain A: S.213, K.214 Chain B: P.104, F.105, M.106, T.107, I.234, Q.238, L.243 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.213, A:S.213, A:K.214, B:T.107 Water bridges: B:T.107, B:Q.238 GOL.11: 11 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, G.140, K.171 Ligands: KAI.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:G.62, B:K.171 Water bridges: B:N.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plested, A.J. et al., Molecular basis of kainate receptor modulation by sodium. Neuron (2008)

Release Date

2008-06-17

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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