SMTL ID : 2xxr.1

Crystal structure of the GluK2 (GluR6) wild-type LBD dimer in complex with glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 10 residues within 4Å: Chain A: Y.61, P.89, L.90, A.91, R.96, G.141, A.142, T.143, E.191, Y.217 13 PLIP interactions: 11 interactions with chain A, 2 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 Water bridges: A:V.138, A:M.144, A:E.191, A:E.191 Salt bridges: A:R.96 GLU.4: 10 residues within 4Å: Chain B: Y.61, P.89, L.90, A.91, R.96, G.141, A.142, T.143, N.174, E.191 13 PLIP interactions: 2 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: E.4, E.4, B:A.91, B:A.142, B:T.143, B:T.143, B:E.191 Hydrophobic interactions: B:Y.61 Water bridges: B:V.138, B:M.144, B:E.191, 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

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

NA.3: 4 residues within 4Å: Chain A: E.97, I.100, D.101, M.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.101 Water bridges: A:F.102 NA.5: 4 residues within 4Å: Chain B: E.97, I.100, D.101, M.223 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.97, B:D.101, B:D.101 Water bridges: B:F.102, B:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayeem, N. et al., Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization. J.Neurosci. (2011)

Release Date

2011-02-09

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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