SMTL ID : 6yk5.1

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound (S)-1-(2'-Amino-2'-carboxyethyl)-5,7-dihydrofuro[3,4-d]- pyrimidine-2,4(1H,3H)-dione at resolution 1.15A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: G.118, T.119, P.120 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.118, A:T.119 GOL.2: 4 residues within 4Å: Chain A: K.116, K.185, G.186 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 GOL.3: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.214, A:D.216, A:S.217 Water bridges: A:S.217, A:S.217, B:D.248 GOL.4: 5 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, C.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.117, A:K.117, A:E.201, A:Q.202 Water bridges: A:K.117, A:C.261 GOL.14: 3 residues within 4Å: Chain B: G.118, T.119, P.120 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.118, B:T.119 GOL.15: 4 residues within 4Å: Chain B: K.116, K.185, G.186 Ligands: SO4.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.185 GOL.16: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.214, B:D.216, B:S.217 Water bridges: B:S.217, B:S.217, A:D.248 GOL.17: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.117, B:K.117, B:E.201, B:Q.202 Water bridges: B:K.117, B:C.261

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

SO4.5: 4 residues within 4Å: Chain A: K.60, A.63, N.72, S.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.72, A:S.140 Water bridges: A:G.141 Salt bridges: A:K.60 SO4.6: 2 residues within 4Å: Chain A: M.18, M.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.19 Water bridges: A:M.19 SO4.7: 2 residues within 4Å: Chain A: R.64, K.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.8: 3 residues within 4Å: Chain A: K.116, R.182 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.116 SO4.9: 3 residues within 4Å: Chain A: H.46, K.240, Q.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.244 Water bridges: A:H.46 Salt bridges: A:H.46 SO4.10: 2 residues within 4Å: Chain A: I.152, A.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.153 Water bridges: A:V.154 SO4.18: 4 residues within 4Å: Chain B: K.60, A.63, N.72, S.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.72, B:S.140 Water bridges: B:G.141 Salt bridges: B:K.60 SO4.19: 2 residues within 4Å: Chain B: M.18, M.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.19 Water bridges: B:M.19 SO4.20: 2 residues within 4Å: Chain B: R.64, K.69 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.64 SO4.21: 3 residues within 4Å: Chain B: K.116, R.182 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.116 SO4.22: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:H.46 Salt bridges: B:H.46 SO4.23: 2 residues within 4Å: Chain B: I.152, A.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.153 Water bridges: B:V.154

2 x LI: LITHIUM ION(Non-covalent)

LI.11: 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.24: 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.19

2 x PVK: (S)-1-(2'-Amino-2'-carboxyethyl)-5,7-dihydrofuro[3,4-d]-pyrimidine-2,4(1H,3H)-dione(Non-covalent)

PVK.12: 14 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, L.192, E.193, M.196, Y.220 13 PLIP interactions: 13 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, A:E.193 Water bridges: A:Y.190, A:Y.190 Salt bridges: A:R.96 PVK.25: 14 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, L.192, E.193, M.196, Y.220 13 PLIP interactions: 13 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, B:E.193 Water bridges: B:Y.190, B:Y.190 Salt bridges: B:R.96

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

CL.13: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: K.4, T.5 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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