SMTL ID : 6yk4.1

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-6-methyl-5 ,7- dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 1.00A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.60, A.63, N.72, S.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.72 Water bridges: A:S.140 Salt bridges: A:K.60 SO4.2: 3 residues within 4Å: Chain A: K.116, R.182 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.3: 2 residues within 4Å: Chain A: R.64, K.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.4: 3 residues within 4Å: Chain A: 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 SO4.13: 4 residues within 4Å: Chain B: K.60, A.63, N.72, S.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.72 Water bridges: B:S.140 Salt bridges: B:K.60 SO4.14: 3 residues within 4Å: Chain B: K.116, R.182 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.116, B:K.116 Salt bridges: B:K.116 SO4.15: 2 residues within 4Å: Chain B: R.64, K.69 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.64 SO4.16: 3 residues within 4Å: Chain A: K.249 Chain B: I.152, A.153 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.153 Water bridges: B:V.154 Salt bridges: A:K.249

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: W.71, V.79, V.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.80, A:Y.80 Water bridges: A:R.64, A:W.71 GOL.6: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.216, A:S.217 Water bridges: A:N.214, A:N.214, A:S.217 GOL.7: 3 residues within 4Å: Chain A: K.185, G.186 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 GOL.8: 5 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, C.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117, A:Q.202 GOL.17: 3 residues within 4Å: Chain B: W.71, V.79, V.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.80, B:Y.80 Water bridges: B:R.64, B:W.71 GOL.18: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.216, B:S.217 Water bridges: B:N.214, B:N.214, B:S.217 GOL.19: 3 residues within 4Å: Chain B: K.185, G.186 Ligands: SO4.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.185 GOL.20: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.117, B:Q.202

2 x LI: LITHIUM ION(Non-covalent)

LI.9: 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.21: 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.20

2 x CG8: (2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5,7-dihydropyrrolo[3,4-d]pyrimidin-1-yl]propanoic acid(Non-covalent)

CG8.10: 15 residues within 4Å: Chain A: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:T.143, A:E.193, A:E.193 Water bridges: A:Y.190, A:Y.190, A:E.193 Salt bridges: A:R.96, A:E.193 CG8.22: 15 residues within 4Å: Chain B: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, B:T.143, B:E.193, B:E.193 Water bridges: B:Y.190, B:Y.190, B:E.193 Salt bridges: B:R.96, B:E.193

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

CL.11: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: M.19 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: M.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frydenvang, K. et al., Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions. Acs Chem Neurosci (2020)

Release Date

2020-06-03

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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