SMTL ID : 6zyu.1 (1 other biounit)

Structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM549

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 1 residues within 4Å: Chain A: D.156 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 ZN.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.15: 1 residues within 4Å: Chain B: D.156 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.156 ZN.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 5 residues within 4Å: Chain A: R.163, A.165, E.166, S.168, F.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.168 Water bridges: A:V.169 CAC.17: 5 residues within 4Å: Chain B: R.163, A.165, E.166, S.168, F.170 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.168 Water bridges: B:V.169

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

ACT.4: 5 residues within 4Å: Chain A: A.134, R.180, S.184, K.187, Y.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.184, A:S.184 Water bridges: A:R.180 Salt bridges: A:R.180 ACT.5: 4 residues within 4Å: Chain A: K.117, E.201, C.261 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.261 Salt bridges: A:K.117 ACT.18: 5 residues within 4Å: Chain B: A.134, R.180, S.184, K.187, Y.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.184, B:S.184 Water bridges: B:R.180 Salt bridges: B:R.180 ACT.19: 4 residues within 4Å: Chain B: K.117, E.201, C.261 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.261 Salt bridges: B:K.117

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.6: 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 15 PLIP interactions: 13 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, A:E.193, E.6, E.6 Water bridges: A:L.138, A:E.193 Salt bridges: A:R.96 GLU.20: 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 15 PLIP interactions: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, B:E.193, E.20, E.20 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

2 x QSZ: (4~{S})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide(Non-covalent)

QSZ.7: 18 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, L.247 Ligands: QSW.8, QSZ.21, QSW.22 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.247, A:P.105 QSZ.21: 18 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Chain B: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Ligands: QSZ.7, QSW.8, QSW.22 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.105, A:L.247

2 x QSW: (4~{R})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide(Non-covalent)

QSW.8: 18 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, L.247 Ligands: QSZ.7, QSZ.21, QSW.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.105, B:P.105, B:L.247 Halogen bonds: A:M.107 QSW.22: 18 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Chain B: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Ligands: QSZ.7, QSW.8, QSZ.21 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.105, A:P.105, A:L.247 Halogen bonds: B:M.107

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: W.71, V.79, Y.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.80, A:Y.80 GOL.10: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.248 Water bridges: B:N.214, B:S.217 GOL.11: 2 residues within 4Å: Chain A: P.205 Ligands: ACT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.205 GOL.23: 3 residues within 4Å: Chain B: W.71, V.79, Y.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.80, B:Y.80 GOL.24: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.214, A:S.217 Hydrogen bonds: B:D.248 GOL.25: 2 residues within 4Å: Chain B: P.205 Ligands: ACT.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.205

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

CL.12: 3 residues within 4Å: Chain A: T.93, V.95, R.96 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: N.29, Y.51 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: K.253 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: T.93, V.95, R.96 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: N.29, Y.51 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: K.253 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Etse, K.S. et al., Development of Thiochroman Dioxide Analogues of Benzothiadiazine Dioxides as New Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors. Acs Chem Neurosci (2021)

Release Date

2021-08-11

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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