SMTL ID : 5cbr.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (S)-2-amino-3-(3,4-dichloro-5-(5-hydroxypyridin-3-yl)phenyl)propanoic acid at 2.0A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 4ZK: 3,4-dichloro-5-(5-hydroxypyridin-3-yl)-L-phenylalanine(Non-covalent)

4ZK.1: 20 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, T.137, L.138, S.142, T.143, T.174, Y.190, L.191, L.192, E.193, M.196, Y.220 Ligands: GOL.3, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:T.91, A:T.91, A:T.91, A:S.142, A:S.142, A:Y.190, A:Y.190, A:E.193 Salt bridges: A:R.96 4ZK.12: 20 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, T.137, L.138, S.142, T.143, T.174, Y.190, L.191, L.192, E.193, M.196, Y.220 Ligands: GOL.14, GOL.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:T.91, B:T.91, B:T.91, B:S.142, B:S.142, B:Y.190, B:Y.190, B:E.193 Salt bridges: B:R.96

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: K.104, P.105, L.239, N.242 Chain B: I.92, P.105, K.218, G.219 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.92, B:I.92, B:G.219, A:N.242 GOL.3: 9 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.72, R.96, S.142 Ligands: 4ZK.1, SO4.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:R.96 Water bridges: A:S.142 GOL.4: 6 residues within 4Å: Chain A: E.13, Y.61, L.138, T.173, T.174 Ligands: 4ZK.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.174, A:T.174 Water bridges: A:A.175 GOL.13: 8 residues within 4Å: Chain A: I.92, P.105, K.218, G.219 Chain B: K.104, P.105, L.239, N.242 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.92, A:I.92, A:G.219, B:N.242 GOL.14: 9 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.72, R.96, S.142 Ligands: 4ZK.12, SO4.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:R.96 Water bridges: B:S.142 GOL.15: 6 residues within 4Å: Chain B: E.13, Y.61, L.138, T.173, T.174 Ligands: 4ZK.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.174, B:T.174 Water bridges: B:A.175

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

SO4.5: 4 residues within 4Å: Chain A: K.144, R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.144 Salt bridges: A:K.144, A:R.148, A:R.163 SO4.6: 3 residues within 4Å: Chain A: K.116, K.185 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.116 SO4.7: 2 residues within 4Å: Chain A: K.151 Chain B: Q.244 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.151 Hydrogen bonds: B:Q.244 SO4.8: 3 residues within 4Å: Chain A: K.116, K.185 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.116 SO4.9: 5 residues within 4Å: Chain A: K.60, N.72, S.140, G.141 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.72, A:S.140, A:G.141 Salt bridges: A:K.60 SO4.10: 4 residues within 4Å: Chain A: K.151, I.152, A.153 Chain B: K.249 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.249 Hydrogen bonds: A:A.153 Water bridges: A:V.154 SO4.16: 4 residues within 4Å: Chain B: K.144, R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.144 Salt bridges: B:K.144, B:R.148, B:R.163 SO4.17: 3 residues within 4Å: Chain B: K.116, K.185 Ligands: SO4.19 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.116 SO4.18: 2 residues within 4Å: Chain A: Q.244 Chain B: K.151 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.244 Salt bridges: B:K.151 SO4.19: 3 residues within 4Å: Chain B: K.116, K.185 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.116 SO4.20: 5 residues within 4Å: Chain B: K.60, N.72, S.140, G.141 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.72, B:S.140, B:G.141 Salt bridges: B:K.60 SO4.21: 4 residues within 4Å: Chain A: K.249 Chain B: K.151, I.152, A.153 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.249 Hydrogen bonds: B:A.153 Water bridges: B:V.154

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 6 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, M.209, C.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.201 Salt bridges: A:K.117 ACT.22: 6 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, M.209, C.261 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.201 Salt bridges: B:K.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szymanska, E. et al., Studies on Aryl-Substituted Phenylalanines: Synthesis, Activity, and Different Binding Modes at AMPA Receptors. J.Med.Chem. (2016)

Release Date

2015-12-30

Peptides

Glutamate receptor 2,Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2,Glutamate receptor 2

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