SMTL ID : 5o9a.1 (1 other biounit)

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y-N775S) in complex with glutamate and BPAM121 at 1.78 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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:D.139, A:S.140 Water bridges: A:S.140, A:K.144, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.2: 1 residues within 4Å: Chain A: K.116 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.116 SO4.3: 3 residues within 4Å: Chain A: K.240 Chain B: Y.94, R.149 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.240, B:R.149 SO4.4: 3 residues within 4Å: Chain A: R.148, W.159, R.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.159 Salt bridges: A:R.148, A:R.163 SO4.13: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.139, B:S.140 Water bridges: B:R.148 Salt bridges: B:K.144, B:R.148 SO4.14: 3 residues within 4Å: Chain B: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.148, B:R.163

2 x 7M6: 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

7M6.5: 15 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Chain B: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Ligands: 7M6.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.105 Hydrogen bonds: B:G.219 Halogen bonds: A:S.108 7M6.15: 15 residues within 4Å: Chain A: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Ligands: 7M6.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.105 Hydrogen bonds: A:G.219

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: L.26 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: S.123, A.124, G.213, L.215 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: K.21, N.22 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: E.33, K.253, W.254, K.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.253, A:K.258 GOL.11: 3 residues within 4Å: Chain A: M.19, H.23, R.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31 GOL.17: 1 residues within 4Å: Chain B: K.258 No protein-ligand interaction detected (PLIP)

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.10: 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: 10 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.10, E.10, E.10, E.10 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.18: 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 12 PLIP interactions: 11 interactions with chain B, 1 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.18 Water bridges: B:E.193, B:E.193 Salt bridges: B:R.96

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 4 residues within 4Å: Chain A: H.46, L.236, K.240 Chain B: Y.94 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.46, B:Y.94, B:Y.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goffin, E. et al., 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors with Nanomolar Potency. J. Med. Chem. (2018)

Release Date

2018-01-03

Peptides

Glutamate receptor 2,Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2,Glutamate receptor 2

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