SMTL ID : 4fat.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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:S.142, A:T.143, A:T.143, A:E.193, E.1, E.1, E.1 Water bridges: A:L.138, A:E.193 Salt bridges: A:R.96 GLU.11: 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:S.142, B:T.143, B:T.143, B:E.193, E.11, E.11, E.11 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

2 x 496: 2-({[4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide(Non-covalent)

496.2: 19 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Chain B: I.92, K.104, P.105, S.217, K.218, G.219, L.239, S.242 Ligands: 496.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.239, B:I.92, B:K.218 Hydrogen bonds: A:F.106, B:S.242 Water bridges: A:S.108 496.12: 19 residues within 4Å: Chain A: I.92, K.104, P.105, 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, L.239, S.242 Ligands: 496.2 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.239, A:I.92, A:K.218 Hydrogen bonds: B:F.106, A:S.242 Water bridges: B:S.108

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

SO4.3: 3 residues within 4Å: Chain A: H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:R.31, A:R.31, A:R.31, A:R.31 Salt bridges: A:H.23, A:R.31 SO4.4: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:E.30, A:E.30 Water bridges: A:N.29, A:N.29 SO4.5: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: GOL.6 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 SO4.13: 3 residues within 4Å: Chain B: H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:R.31, B:R.31, B:R.31, B:R.31 Salt bridges: B:H.23, B:R.31 SO4.14: 4 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.29, B:N.29, B:E.30, B:E.30 Water bridges: B:N.29, B:N.29 SO4.15: 6 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 Ligands: GOL.16 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: G.62, A.63, W.71, T.93, V.95, R.96, S.140, G.141, E.145 Ligands: SO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:R.96, A:R.96 Water bridges: A:R.64 GOL.7: 3 residues within 4Å: Chain A: R.148, W.159, R.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.148, A:R.163, A:R.163 GOL.8: 6 residues within 4Å: Chain A: S.108, L.109, S.194, T.195, E.198, N.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:N.214 Water bridges: A:E.198, A:E.198 GOL.9: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.216 Water bridges: B:S.217 GOL.16: 10 residues within 4Å: Chain B: G.62, A.63, W.71, T.93, V.95, R.96, S.140, G.141, E.145 Ligands: SO4.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.93, B:T.93, B:R.96, B:R.96 Water bridges: B:R.64 GOL.17: 3 residues within 4Å: Chain B: R.148, W.159, R.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.148, B:R.163, B:R.163 GOL.18: 6 residues within 4Å: Chain B: S.108, L.109, S.194, T.195, E.198, N.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.194, B:S.194, B:N.214 Water bridges: B:E.198, B:E.198 GOL.19: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:S.217

2 x LI: LITHIUM ION(Non-covalent)

LI.10: 3 residues within 4Å: Chain A: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.97, A:E.97, A:I.100, H2O.2 LI.20: 3 residues within 4Å: Chain B: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, B:I.100, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harms, J.E. et al., Functional analysis of a novel positive allosteric modulator of AMPA receptors derived from a structure-based drug design strategy. Neuropharmacology (2013)

Release Date

2012-07-11

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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