SMTL ID : 4g8n.1

Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist G8M

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x G8M: (1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid(Non-covalent)

G8M.1: 12 residues within 4Å: Chain A: Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191, Y.217 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.63, A:Y.63, A:V.139 Hydrogen bonds: A:P.90, A:T.92, A:T.92, A:A.143, A:T.144, A:T.144 Water bridges: A:M.145, A:E.191 Salt bridges: A:R.97 G8M.6: 12 residues within 4Å: Chain B: Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191, Y.217 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.63, B:Y.63, B:V.139 Hydrogen bonds: B:P.90, B:T.92, B:T.92, B:T.92, B:A.143, B:T.144 Water bridges: B:T.144, B:T.144, B:M.145 Salt bridges: B:R.97

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

CL.2: 3 residues within 4Å: Chain A: R.33, R.56, L.57 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.33, R.56, L.57 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: S.24, R.26 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.24, A:R.26, H2O.3, H2O.3, H2O.5 K.5: 2 residues within 4Å: Chain A: N.5, S.52 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.5, A:S.52, H2O.1 K.9: 2 residues within 4Å: Chain B: S.24, R.26 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.24, B:R.26, H2O.8, H2O.8, H2O.10 K.10: 2 residues within 4Å: Chain B: N.5, S.52 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.5, B:S.52, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juknaite, L. et al., Pharmacological and structural characterization of conformationally restricted (S)-glutamate analogues at ionotropic glutamate receptors. J.Struct.Biol. (2012)

Release Date

2012-08-29

Peptides

Glutamate receptor, ionotropic kainate 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor, ionotropic kainate 3

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