SMTL ID : 4iy6.1

Crystal structure of the GLUA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and ME-CX516 at 1.72 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x MQR: [(3R)-3-methylpiperidin-1-yl](quinoxalin-6-yl)methanone(Non-covalent)

MQR.1: 16 residues within 4Å: Chain A: P.105, F.106, M.107, S.108, S.217, K.218, S.242, L.247 Chain B: P.105, F.106, M.107, S.108, S.217, K.218, G.219 Ligands: MQR.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.105, A:L.247, B:P.105 Water bridges: A:L.109 MQR.8: 16 residues within 4Å: Chain A: P.105, F.106, M.107, S.108, S.217, K.218, G.219 Chain B: P.105, F.106, M.107, S.108, S.217, K.218, S.242, L.247 Ligands: MQR.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.105, B:L.247, A:P.105 Water bridges: B:L.109

4 x MQS: [(3S)-3-methylpiperidin-1-yl](quinoxalin-6-yl)methanone(Non-covalent)

MQS.2: 7 residues within 4Å: Chain A: S.128, K.129, Q.130, T.131, I.133, Y.135, Y.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.131, A:Y.161 pi-Stacking: A:Y.161 MQS.3: 9 residues within 4Å: Chain A: K.116, K.117, G.118, T.119, P.120, K.185, G.186, K.187 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.116, A:P.120, A:K.187 MQS.9: 7 residues within 4Å: Chain B: S.128, K.129, Q.130, T.131, I.133, Y.135, Y.161 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.131, B:Y.161 pi-Stacking: B:Y.161 MQS.10: 9 residues within 4Å: Chain B: K.116, K.117, G.118, T.119, P.120, K.185, G.186, K.187 Ligands: SO4.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.116, B:P.120, B:K.187

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 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.4, E.4, E.4 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 GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.12: 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

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

SO4.6: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:K.144, A:K.144, A:E.145, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.7: 2 residues within 4Å: Chain A: K.116 Ligands: MQS.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.116 Salt bridges: A:K.116 SO4.13: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:K.144, B:K.144, B:E.145, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.14: 2 residues within 4Å: Chain B: K.116 Ligands: MQS.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.116 Salt bridges: B:K.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krintel, C. et al., Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-10-09

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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