SMTL ID : 6yk2.1

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound (S)-1-[2'-Amino-2'-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin- 2,4(1H,3H)-dione at resolution 1.60A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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 SO4.2: 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 SO4.3: 2 residues within 4Å: Chain A: M.18, M.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.19 SO4.11: 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 SO4.12: 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 SO4.13: 2 residues within 4Å: Chain B: M.18, M.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.19

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: W.71, V.79, V.99 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.69, A:Y.80 GOL.5: 2 residues within 4Å: Chain A: K.185, G.186 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.185 GOL.6: 3 residues within 4Å: Chain A: K.151, I.152, A.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.153 GOL.7: 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:K.117, A:Q.202 GOL.8: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.216, B:S.217 Water bridges: B:S.217 GOL.14: 3 residues within 4Å: Chain B: W.71, V.79, V.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.69, B:Y.80 GOL.15: 2 residues within 4Å: Chain B: K.185, G.186 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.185 GOL.16: 3 residues within 4Å: Chain B: K.151, I.152, A.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.153 GOL.17: 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:K.117, B:Q.202 GOL.18: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.216, A:S.217 Water bridges: A:S.217

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

CGW.9: 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 9 PLIP interactions: 9 interactions with chain A 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 CGW.19: 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 9 PLIP interactions: 9 interactions with chain B 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 CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.20: 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,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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