SMTL ID : 3c34.1

Crystal structure of GluR5 ligand-binding core in complex with rubidium at 1.82 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

6 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 3 residues within 4Å: Chain A: E.96, I.99, D.100 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.96, A:I.99, A:D.100, H2O.11, H2O.11 RB.2: 1 residues within 4Å: Chain A: S.22 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.22, H2O.11 RB.3: 1 residues within 4Å: Chain A: L.181 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.181 RB.4: 3 residues within 4Å: Chain A: K.150, S.152, E.155 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.150 RB.10: 3 residues within 4Å: Chain B: E.96, I.99, D.100 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.96, B:I.99, B:D.100, H2O.21 RB.11: 3 residues within 4Å: Chain B: T.118, I.120, D.121 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.118, B:I.120, B:D.121, H2O.15

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

CL.5: 4 residues within 4Å: Chain A: K.103, R.227 Chain B: K.103, R.227 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.31, K.54, L.55 Ligands: GOL.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.31, K.54, L.55 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.20, S.22 Ligand excluded by PLIP

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

KAI.7: 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, E.190, Y.216 Ligands: GOL.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.13, A:Y.61, A:V.137 Hydrogen bonds: A:T.90, A:T.90, A:S.141, A:S.141, A:T.142, A:E.190 Water bridges: 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, G.140, S.141, T.142, E.190 Ligands: GOL.15 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.61 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:G.140, B:E.190 Salt bridges: B:R.95

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, G.140 Ligands: KAI.7 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.9: 4 residues within 4Å: Chain A: K.54, L.55, P.57 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.55 GOL.15: 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.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:G.62, B:K.171 Water bridges: B:G.59, 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

Related Entries With Identical Sequence