SMTL ID : 6yk3.1

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-5 ,7- dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 1.20A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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: 6 residues within 4Å: Chain A: D.248 Chain B: G.213, N.214, L.215, D.216, S.217 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.216 Water bridges: B:G.213, B:N.214, B:N.214, B:S.217 GOL.3: 7 residues within 4Å: Chain A: I.11, E.13, Y.61, L.138, T.173, T.174 Ligands: PVQ.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.12, A:Y.61, A:T.174, A:T.174 Water bridges: A:A.175 GOL.4: 5 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, C.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.117, A:Q.202 Water bridges: A:K.117 GOL.13: 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.14: 6 residues within 4Å: Chain A: G.213, N.214, L.215, D.216, S.217 Chain B: D.248 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:G.213, A:N.214, A:N.214, A:S.217 GOL.15: 7 residues within 4Å: Chain B: I.11, E.13, Y.61, L.138, T.173, T.174 Ligands: PVQ.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.12, B:Y.61, B:T.174, B:T.174 Water bridges: B:A.175 GOL.16: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.117, B:Q.202 Water bridges: B:K.117

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

SO4.5: 2 residues within 4Å: Chain A: K.116, R.182 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.6: 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, A:S.140 Salt bridges: A:K.60 SO4.7: 2 residues within 4Å: Chain A: R.64, K.69 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.69, A:K.69 Salt bridges: A:R.64, A:K.69 SO4.8: 3 residues within 4Å: Chain A: K.249 Chain B: I.152, A.153 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.153 Water bridges: B:V.154, A:K.249 Salt bridges: A:K.249 SO4.17: 2 residues within 4Å: Chain B: K.116, R.182 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.116, B:K.116 Salt bridges: B:K.116 SO4.18: 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, B:S.140 Salt bridges: B:K.60 SO4.19: 2 residues within 4Å: Chain B: R.64, K.69 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.69, B:K.69 Salt bridges: B:R.64, B:K.69 SO4.20: 3 residues within 4Å: Chain A: I.152, A.153 Chain B: K.249 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.153 Water bridges: A:V.154, B:K.249 Salt bridges: B:K.249

2 x PVQ: (S)-1-[2'-Amino-2'-carboxyethyl]-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione(Non-covalent)

PVQ.9: 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, L.192, E.193, M.196, Y.220 Ligands: GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:T.143, A:E.193, A:E.193 Salt bridges: A:R.96 PVQ.21: 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, L.192, E.193, M.196, Y.220 Ligands: GOL.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:T.143, B:E.193, B:E.193 Salt bridges: B:R.96

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.10: 3 residues within 4Å: Chain A: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.97 Water bridges: A:F.102, A:K.226, B:N.235 NH4.22: 3 residues within 4Å: Chain B: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.101 Water bridges: B:F.102, B:K.226, A:N.235

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: 2 residues within 4Å: Chain A: M.18, M.19 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: M.18, 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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