SMTL ID : 5cmk.1

Crystal structure of the GluK2EM LBD dimer assembly complex with glutamate and LY466195

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 13 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, V.138, G.141, S.142, T.143, M.144, M.190, E.191, Y.217 14 PLIP interactions: 2 Ligand-Ligand interactions, 12 interactions with chain A Hydrogen bonds: E.1, E.1, A:T.91, A:T.91, A:S.142, A:T.143, A:T.143 Hydrophobic interactions: A:Y.61 Water bridges: A:V.138, A:G.141, A:E.191, A:E.191, A:Y.217 Salt bridges: A:R.96

2 x LI: LITHIUM ION(Non-covalent)

LI.2: 6 residues within 4Å: Chain A: E.97, I.100, D.101, F.102, M.223 Chain B: I.233 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.97, A:E.97, A:I.100, H2O.1 LI.5: 5 residues within 4Å: Chain B: E.97, I.100, D.101, F.102, M.223 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, B:I.100, H2O.10

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

CL.3: 5 residues within 4Å: Chain A: K.104, R.228, T.232 Chain B: K.104, R.228 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: N.3, R.4 Ligand excluded by PLIP

1 x LY5: (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid(Non-covalent)

LY5.4: 16 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, V.138, G.141, S.142, T.143, S.174, M.190, E.191, T.194, Y.217 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.61, B:V.138 Hydrogen bonds: B:P.89, B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:E.191 Water bridges: B:G.62, B:T.91, B:G.141 Salt bridges: B:R.96, B:E.191

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain B: K.24, P.25, L.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.26 Water bridges: B:R.31, B:R.31, B:R.31 SO4.7: 2 residues within 4Å: Chain B: R.54, E.57 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.54, B:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyerson, J.R. et al., Structural basis of kainate subtype glutamate receptor desensitization. Nature (2016)

Release Date

2016-07-20

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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