SMTL ID : 3g3k.1

Crystal structure of the GluR6 ligand binding domain dimer I442H K494E K665R I749L Q753K E757Q mutant with glutamate and NaCl at 1.24 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 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 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:A.91, A:A.142, A:T.143, A:T.143, A:E.191, E.1, E.1, E.1 Water bridges: A:V.138, A:V.138, A:E.191, A:E.191 Salt bridges: A:R.96 GLU.8: 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, E.8 Water bridges: B:V.138, B:V.138, B:E.191, B:E.191 Salt bridges: B:R.96

5 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 CL.3: 5 residues within 4Å: Chain A: Q.239, G.242, K.243, L.244, H.245 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.94, R.149 Chain B: K.237 Ligands: IPA.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.117, G.118, T.206 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: Q.239, G.242, K.243, L.244, H.245 Ligand excluded by PLIP

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

NA.5: 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:E.97, A:D.101 Water bridges: A:F.102 NA.11: 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

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

IPA.6: 9 residues within 4Å: Chain A: P.105, T.108, S.214, K.215, G.216 Chain B: P.105, M.107, T.108, Q.239 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.108 IPA.7: 6 residues within 4Å: Chain A: Q.64, Y.94, V.95, E.98, R.149 Ligands: CL.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.95 Hydrogen bonds: A:Y.94, A:E.98

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