SMTL ID : 3pmx.1

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, E.1, E.1, E.1 Water bridges: A:K.144, A:E.193 Salt bridges: A:R.96 GLU.15: 11 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, E.15, E.15, E.15 Water bridges: B:K.144, B:E.193 Salt bridges: B:R.96

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

SO4.2: 4 residues within 4Å: Chain A: H.23, E.24, R.31 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.23, A:R.31 SO4.3: 4 residues within 4Å: Chain A: D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:A.63, A:K.144, A:K.144 Salt bridges: A:K.144, A:R.148 SO4.4: 5 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.29, A:E.30 SO4.5: 4 residues within 4Å: Chain A: E.24, L.26, R.31 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24 Salt bridges: A:R.31 SO4.16: 4 residues within 4Å: Chain B: H.23, E.24, R.31 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.23, B:R.31 SO4.17: 4 residues within 4Å: Chain B: D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:A.63, B:K.144, B:K.144 Salt bridges: B:K.144, B:R.148 SO4.18: 5 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.29, B:E.30 SO4.19: 4 residues within 4Å: Chain B: E.24, L.26, R.31 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.24 Salt bridges: B:R.31

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.148, R.149, W.159, R.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.149 GOL.7: 7 residues within 4Å: Chain A: S.108, L.109, S.194, T.195, E.198, K.210, N.214 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.198, A:K.210, A:K.210, A:N.214 Water bridges: A:S.108, A:L.109, A:L.109 GOL.20: 4 residues within 4Å: Chain B: R.148, R.149, W.159, R.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.149 GOL.21: 7 residues within 4Å: Chain B: S.108, L.109, S.194, T.195, E.198, K.210, N.214 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.198, B:K.210, B:K.210, B:N.214 Water bridges: B:S.108, B:L.109, B:L.109

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 5 residues within 4Å: Chain A: M.107, S.108, K.251 Chain B: S.217 Ligands: 808.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.217, A:S.108 DMS.9: 6 residues within 4Å: Chain A: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.4 Salt bridges: A:D.84 DMS.22: 5 residues within 4Å: Chain A: S.217 Chain B: M.107, S.108, K.251 Ligands: 808.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.108, A:S.217 DMS.23: 6 residues within 4Å: Chain B: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.4 Salt bridges: B:D.84

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 7 residues within 4Å: Chain A: G.62, A.63, T.93, V.95, R.96, G.141, E.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.93, A:T.93 Water bridges: A:G.141, A:E.145 EDO.11: 5 residues within 4Å: Chain A: S.242, E.243 Chain B: F.146, D.216, K.218 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.216 Water bridges: B:S.217, B:K.218, A:S.242, A:E.243, A:E.243, A:E.243 EDO.12: 4 residues within 4Å: Chain A: N.29, K.50, Y.51 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:Y.51 Water bridges: A:Y.51 EDO.13: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.217 Water bridges: A:S.217 EDO.24: 7 residues within 4Å: Chain B: G.62, A.63, T.93, V.95, R.96, G.141, E.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.93, B:T.93 Water bridges: B:G.141, B:E.145 EDO.25: 5 residues within 4Å: Chain A: F.146, D.216, K.218 Chain B: S.242, E.243 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.216 Water bridges: A:S.217, A:K.218, B:S.242, B:E.243, B:E.243, B:E.243 EDO.26: 4 residues within 4Å: Chain B: N.29, K.50, Y.51 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.29, B:Y.51 Water bridges: B:Y.51 EDO.27: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.217 Water bridges: B:S.217

2 x 808: N-[(2S)-5-{[5-(trifluoromethyl)furan-2-yl]methyl}-2,3-dihydro-1H-inden-2-yl]propane-2-sulfonamide(Non-covalent)

808.14: 19 residues within 4Å: Chain A: I.92, K.104, P.105, S.217, K.218, G.219, L.239 Chain B: I.92, K.104, P.105, M.107, S.108, K.218, G.219, V.238, L.239, S.242 Ligands: DMS.22, 808.28 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.105, B:V.238, A:P.105 Hydrogen bonds: B:P.105, A:G.219 Halogen bonds: B:G.219 808.28: 19 residues within 4Å: Chain A: I.92, K.104, P.105, M.107, S.108, K.218, G.219, V.238, L.239, S.242 Chain B: I.92, K.104, P.105, S.217, K.218, G.219, L.239 Ligands: DMS.8, 808.14 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.105, A:V.238, B:P.105 Hydrogen bonds: A:P.105, B:G.219 Halogen bonds: A:G.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamieson, C. et al., Structure based evolution of a novel series of positive modulators of the AMPA receptor. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-01-12

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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