SMTL ID : 3g3f.1

Crystal structure of the GluR6 ligand binding domain dimer with glutamate and NaCl at 1.38 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 14 residues within 4Å: Chain A: Y.61, P.89, L.90, A.91, R.96, V.138, G.141, A.142, T.143, M.144, N.174, M.190, E.191, Y.217 15 PLIP interactions: 12 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:P.89, A:A.91, A:A.142, A:T.143, A:T.143, E.1, E.1, E.1 Water bridges: A:V.138, A:V.138, A:N.174, A:E.191, A:E.191 Salt bridges: A:R.96 GLU.5: 14 residues within 4Å: Chain B: Y.61, P.89, L.90, A.91, R.96, V.138, G.141, A.142, T.143, M.144, N.174, M.190, E.191, Y.217 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:P.89, B:P.89, B:A.91, B:A.142, B:T.143, B:T.143, B:E.191, E.5 Water bridges: B:V.138, B:V.138, B:E.191 Salt bridges: B:R.96

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

CL.2: 4 residues within 4Å: Chain A: K.104, R.228 Chain B: K.104, R.228 Ligand excluded by PLIP

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

NA.3: 4 residues within 4Å: Chain A: E.97, I.100, D.101, M.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.101, A:D.101 Water bridges: A:F.102 NA.6: 4 residues within 4Å: Chain B: E.97, I.100, D.101, M.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.101 Water bridges: B:F.102 NA.7: 1 residues within 4Å: Chain B: S.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.22, B:S.22 NA.8: 2 residues within 4Å: Chain B: I.11, L.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.12, B:L.12

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 7 residues within 4Å: Chain A: Q.237, E.240, E.241 Chain B: Y.94, V.95, K.149, K.151 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.94 IPA.9: 5 residues within 4Å: Chain A: Y.94, K.149 Chain B: Q.237, E.240, E.241 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.240, A:Y.94 Water bridges: B:E.240, A:K.149, A:K.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaudhry, C. et al., Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization. Embo J. (2009)

Release Date

2009-06-02

Peptides

Glutamate receptor, ionotropic kainate 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor, ionotropic kainate 2

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