SMTL ID : 3c32.1

Crystal structure of GluR5 ligand-binding core in complex with sodium at 1.72 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: E.96, I.99, D.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.100 NA.6: 3 residues within 4Å: Chain B: E.96, I.99, D.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.96, B:I.99, 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.7: 3 residues within 4Å: Chain B: E.69, W.70, K.75 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.31, K.54, L.55 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, V.137, G.140, S.141, T.142, E.190 Ligands: GOL.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.61, A:V.137 Hydrogen bonds: A:T.90, A:T.90, A:S.141, A:S.141, A:T.142, A:T.142, A:E.190 Water bridges: A:M.143, A:E.190 Salt bridges: A:R.95 KAI.9: 13 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, Y.216 Ligands: GOL.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.61, B:V.137 Hydrogen bonds: B:T.90, B:S.141, 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

4 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:G.62, A:K.171 Water bridges: A:N.71 GOL.10: 10 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, K.171 Ligands: KAI.9 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 GOL.11: 9 residues within 4Å: Chain A: T.107, S.213, K.214 Chain B: P.104, F.105, M.106, T.107, 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.12: 7 residues within 4Å: Chain B: E.14, S.173, D.174, I.177, M.189, S.193, Y.196 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.14, B:S.173, B:D.174, B:S.193 Water bridges: B:E.13, B:E.13

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

Related Entries With Identical Sequence