SMTL ID : 4mh5.1

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 10 residues within 4Å: Chain A: Y.63, P.90, L.91, T.92, R.97, G.142, A.143, T.144, E.191, Y.217 16 PLIP interactions: 13 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:P.90, A:T.92, A:T.92, A:T.92, A:A.143, A:T.144, A:T.144, E.1, E.1, E.1 Water bridges: A:V.139, A:V.139, A:V.139, A:E.191 Salt bridges: A:R.97 GLU.7: 10 residues within 4Å: Chain B: Y.63, P.90, L.91, T.92, R.97, G.142, A.143, T.144, E.191, Y.217 16 PLIP interactions: 13 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.63 Hydrogen bonds: B:P.90, B:T.92, B:T.92, B:A.143, B:T.144, B:T.144, E.7, E.7, E.7 Water bridges: B:V.139, B:V.139, B:V.139, B:E.191, B:Y.217 Salt bridges: B:R.97

4 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: N.5, S.52 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.5, A:S.52 K.3: 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.6, H2O.11, H2O.11 K.8: 2 residues within 4Å: Chain B: N.5, S.52 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.5, B:S.52 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.18, H2O.22, H2O.22

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

CL.4: 3 residues within 4Å: Chain A: R.33, R.56, L.57 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.33, R.56, L.57 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: K.99 Chain B: T.109 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.99, B:T.109 GOL.12: 2 residues within 4Å: Chain A: T.109 Chain B: K.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venskutonyte, R. et al., Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate. J.Struct.Biol. (2011)

Release Date

2013-10-16

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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