SMTL ID : 3pmv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, E.1, E.1, E.1 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.12: 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, E.12, E.12, E.12 Water bridges: B:E.193 Salt bridges: B:R.96

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

SO4.2: 4 residues within 4Å: Chain A: H.23, E.24, R.31 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:Y.32 Salt bridges: A:H.23, A:R.31 SO4.3: 5 residues within 4Å: Chain A: E.27, G.28, N.29, E.30, K.52 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:E.30 Water bridges: A:E.30, A:K.52, A:K.52 Salt bridges: A:K.52 SO4.4: 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:D.139, A:S.140 Water bridges: A:K.144, A:K.144 Salt bridges: A:K.144, A:R.148 SO4.5: 3 residues within 4Å: Chain A: E.24, R.31 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.28 Salt bridges: A:R.31 SO4.6: 1 residues within 4Å: Chain A: K.82 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.82 SO4.13: 4 residues within 4Å: Chain B: H.23, E.24, R.31 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:Y.32 Salt bridges: B:H.23, B:R.31 SO4.14: 5 residues within 4Å: Chain B: E.27, G.28, N.29, E.30, K.52 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.29, B:N.29, B:E.30 Water bridges: B:E.30, B:K.52, B:K.52 Salt bridges: B:K.52 SO4.15: 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:D.139, B:S.140 Water bridges: B:K.144, B:K.144 Salt bridges: B:K.144, B:R.148 SO4.16: 3 residues within 4Å: Chain B: E.24, R.31 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.28 Salt bridges: B:R.31 SO4.17: 1 residues within 4Å: Chain B: K.82 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82

2 x 557: N-[(2S)-2-{4-[4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}propyl]propane-2-sulfonamide(Non-covalent)

557.7: 20 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, S.242, L.247 Chain B: K.104, P.105, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Ligands: 557.18 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.92, A:P.105, B:P.105, B:P.105 Water bridges: A:G.219, A:G.219 Hydrogen bonds: B:P.105 557.18: 20 residues within 4Å: Chain A: K.104, P.105, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, S.242, L.247 Ligands: 557.7 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.92, B:P.105, A:P.105, A:P.105 Water bridges: B:G.219, B:G.219 Hydrogen bonds: A:P.105

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: S.108, L.109, S.194, T.195, E.198, N.214 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.108, A:S.194, A:N.214 Water bridges: A:S.108, A:S.108, A:L.109 GOL.9: 3 residues within 4Å: Chain A: R.203, K.258, E.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.203, A:R.203, A:E.260 Water bridges: A:D.257, A:K.258 GOL.10: 3 residues within 4Å: Chain A: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.148 GOL.11: 3 residues within 4Å: Chain A: K.116, K.185, G.186 No protein-ligand interaction detected (PLIP) GOL.19: 6 residues within 4Å: Chain B: S.108, L.109, S.194, T.195, E.198, N.214 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.108, B:S.194, B:N.214 Water bridges: B:S.108, B:S.108, B:L.109 GOL.20: 3 residues within 4Å: Chain B: R.203, K.258, E.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.203, B:R.203, B:E.260 Water bridges: B:D.257, B:K.258 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.148 GOL.22: 3 residues within 4Å: Chain B: K.116, K.185, G.186 No protein-ligand interaction detected (PLIP)

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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