SMTL ID : 3s9e.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 14 residues within 4Å: Chain A: Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, M.145, N.174, M.190, E.191, Y.217 17 PLIP interactions: 15 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:P.90, A:T.92, A:T.92, A:A.143, A:T.144, A:T.144, E.1, E.1 Water bridges: A:V.139, A:V.139, A:V.139, A:N.174, A:E.191, A:E.191, A:Y.217 Salt bridges: A:R.97 GLU.8: 14 residues within 4Å: Chain B: Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, M.145, N.174, M.190, E.191, Y.217 17 PLIP interactions: 3 Ligand-Ligand interactions, 14 interactions with chain B Hydrogen bonds: E.8, E.8, E.8, B:T.92, B:T.92, B:A.143, B:T.144, B:T.144 Hydrophobic interactions: B:Y.63 Water bridges: B:V.139, B:V.139, B:V.139, B:N.174, B:E.191, B:E.191, B:Y.217 Salt bridges: B:R.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: H.95, K.99 Chain B: T.109 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.99, B:T.109 Water bridges: A:H.95, A:H.95, A:H.95

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

CL.3: 5 residues within 4Å: Chain A: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.33, F.34, R.56, L.57 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: Q.239, D.242, K.243, L.244, H.245 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.33, F.34, R.56, L.57 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 2 residues within 4Å: Chain A: K.62, K.140 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.73, A:N.73 Salt bridges: A:K.62, A:K.140 PO4.6: 1 residues within 4Å: Chain A: K.250 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.40 Salt bridges: A:K.250 PO4.11: 2 residues within 4Å: Chain B: K.62, K.140 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.62, B:K.62, B:N.73 Salt bridges: B:K.62, B:K.140

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

NA.7: 4 residues within 4Å: Chain A: S.24, R.26, T.27, L.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.24 Water bridges: A:S.24 NA.12: 4 residues within 4Å: Chain B: S.24, R.26, T.27, L.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.26 Water bridges: B:S.24 NA.13: 2 residues within 4Å: Chain B: N.5, S.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.5 Water bridges: B:S.52

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

2011-09-28

Peptides

Glutamate receptor, ionotropic kainate 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor, ionotropic kainate 3

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