SMTL ID : 5fhm.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: M.107, S.108, D.248, K.251 Chain B: S.217 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.108, A:S.108, A:S.108 SO4.2: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Water bridges: A:S.140, A:K.144 Salt bridges: A:K.144, A:R.148 SO4.3: 2 residues within 4Å: Chain A: R.64, K.69 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.64, A:R.64 Salt bridges: A:R.64, A:K.69 SO4.14: 6 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, S.142 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.91, B:T.91, B:T.91, B:S.142 Water bridges: B:S.142, B:S.142, B:E.193, B:E.193 Salt bridges: B:R.96 SO4.15: 4 residues within 4Å: Chain B: K.144, R.148, W.159, R.163 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.144, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148, B:R.163 SO4.16: 2 residues within 4Å: Chain B: E.13, S.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:S.14

1 x 5XP: (2~{S})-3-[5-[2-[[3-(aminomethyl)phenyl]methyl]-1,2,3,4-tetrazol-5-yl]-3-oxidanyl-1,2-oxazol-4-yl]-2-azanyl-propanoic acid(Non-covalent)

5XP.4: 23 residues within 4Å: Chain A: E.13, S.14, P.15, Y.16, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, T.195, M.196, Y.199, I.200, Y.220, W.255 Ligands: EDO.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.16, A:Y.61, A:L.138, A:M.196 Hydrogen bonds: A:E.13, A:S.14, A:P.89, A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:T.143, A:E.193, A:Y.220 Water bridges: A:T.137, A:L.138, A:G.141 Salt bridges: A:R.96

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.248, N.252 Chain B: N.214, L.215, D.216, S.217 Ligands: SO4.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.252, B:N.214, B:D.216 GOL.17: 4 residues within 4Å: Chain B: K.116, K.117, K.185, G.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.116

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

ACT.6: 3 residues within 4Å: Chain A: I.152, A.153 Chain B: K.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.153 Water bridges: A:V.154 ACT.18: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.46, B:K.240 Salt bridges: B:H.46, B:K.240 ACT.19: 4 residues within 4Å: Chain A: K.249 Chain B: K.151, I.152, A.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.151, B:A.153 ACT.20: 3 residues within 4Å: Chain B: K.20, N.22, L.26 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.20, B:K.20 Salt bridges: B:K.20

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: L.12, E.13, S.14 Ligands: 5XP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.13, A:S.14, A:S.14 EDO.8: 3 residues within 4Å: Chain A: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.148, A:W.159, A:R.163 Water bridges: A:R.163 EDO.9: 6 residues within 4Å: Chain A: K.144, R.148, W.159, R.163, F.170 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.144, A:R.163, A:R.163 EDO.10: 3 residues within 4Å: Chain A: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.46, A:K.240, A:Q.244 Water bridges: A:K.45 EDO.11: 3 residues within 4Å: Chain A: K.116, K.185, G.186 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.116 EDO.21: 7 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.72, R.96, G.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:G.62, B:R.96 EDO.22: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:S.217

2 x LI: LITHIUM ION(Non-covalent)

LI.12: 3 residues within 4Å: Chain A: N.242, D.248 Chain B: S.217 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.217, B:S.217, H2O.3, H2O.4 LI.13: 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.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S.Y. et al., Tweaking Subtype Selectivity and Agonist Efficacy at (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) Receptors in a Small Series of BnTetAMPA Analogues. J.Med.Chem. (2016)

Release Date

2016-03-02

Peptides

Glutamate receptor 2,Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2,Glutamate receptor 2

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