SMTL ID : 3pmw.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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 13 PLIP interactions: 10 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:S.142, A:T.143, A:T.143, A:E.193, A:E.193, E.1, E.1, E.1 Salt bridges: A:R.96 GLU.13: 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 13 PLIP interactions: 10 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:S.142, B:T.143, B:T.143, B:E.193, B:E.193, E.13, E.13, E.13 Salt bridges: B:R.96

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

SO4.2: 4 residues within 4Å: Chain A: D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:S.140, A:G.141 Salt bridges: A:K.144, A:R.148 SO4.3: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:E.30 SO4.4: 3 residues within 4Å: Chain A: H.46, K.240 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.46, A:K.240 SO4.5: 2 residues within 4Å: Chain A: Y.199, R.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.14, A:Y.199 Water bridges: A:K.204 Salt bridges: A:R.203 SO4.6: 5 residues within 4Å: Chain A: H.46, K.240, Q.244 Ligands: SO4.4, GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.244 Salt bridges: A:H.46, A:K.240 SO4.7: 3 residues within 4Å: Chain A: R.203, K.258, E.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.260 Salt bridges: A:R.203, A:K.258 SO4.8: 4 residues within 4Å: Chain A: S.108, S.194, E.198, N.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194, A:E.198, A:N.214 SO4.14: 4 residues within 4Å: Chain B: D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:S.140, B:G.141 Salt bridges: B:K.144, B:R.148 SO4.15: 4 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.29, B:N.29, B:E.30 SO4.16: 3 residues within 4Å: Chain B: H.46, K.240 Ligands: SO4.18 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.46, B:K.240 SO4.17: 2 residues within 4Å: Chain B: Y.199, R.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.14, B:Y.199 Water bridges: B:K.204 Salt bridges: B:R.203 SO4.18: 5 residues within 4Å: Chain B: H.46, K.240, Q.244 Ligands: SO4.16, GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.244 Salt bridges: B:H.46, B:K.240 SO4.19: 3 residues within 4Å: Chain B: R.203, K.258, E.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.260 Salt bridges: B:R.203, B:K.258 SO4.20: 4 residues within 4Å: Chain B: S.108, S.194, E.198, N.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.194, B:E.198, B:N.214

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 GOL.10: 3 residues within 4Å: Chain A: Q.244 Chain B: K.151 Ligands: SO4.6 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain B: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.163 GOL.22: 3 residues within 4Å: Chain A: K.151 Chain B: Q.244 Ligands: SO4.18 No protein-ligand interaction detected (PLIP)

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

DMS.11: 5 residues within 4Å: Chain A: M.107, S.108 Chain B: S.217 Ligands: G69.12, G69.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.108 DMS.23: 5 residues within 4Å: Chain A: S.217 Chain B: M.107, S.108 Ligands: G69.12, G69.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.108

2 x G69: N-[(2S)-5-{[4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-2,3-dihydro-1H-inden-2-yl]propane-2-sulfonami de(Non-covalent)

G69.12: 24 residues within 4Å: Chain A: I.92, K.104, P.105, M.107, S.108, S.217, K.218, G.219, V.238, L.239, S.242 Chain B: I.92, K.104, P.105, S.108, S.217, K.218, G.219, V.238, L.239, S.242 Ligands: DMS.11, DMS.23, G69.24 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:P.105, A:K.104, A:P.105, A:P.105, A:V.238, A:L.239 Hydrogen bonds: B:G.219, A:P.105 Halogen bonds: A:G.219 G69.24: 24 residues within 4Å: Chain A: I.92, K.104, P.105, S.108, S.217, K.218, G.219, V.238, L.239, S.242 Chain B: I.92, K.104, P.105, M.107, S.108, S.217, K.218, G.219, V.238, L.239, S.242 Ligands: DMS.11, G69.12, DMS.23 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.104, B:P.105, B:P.105, B:V.238, B:L.239, A:P.105 Hydrogen bonds: B:P.105, A:G.219 Halogen bonds: B: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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