SMTL ID : 5ng9.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist CIP-AS at 1.15 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

4 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 4 residues within 4Å: Chain A: M.19, H.23, R.31 Ligands: FLC.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31 Salt bridges: A:H.23, A:H.23, A:R.31 FLC.2: 2 residues within 4Å: Chain A: R.31 Ligands: FLC.1 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.31, A:R.31, A:Y.32, A:Y.32 Salt bridges: A:R.31, A:R.31 FLC.10: 4 residues within 4Å: Chain B: M.19, H.23, R.31 Ligands: FLC.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.31 Salt bridges: B:H.23, B:H.23, B:R.31 FLC.11: 2 residues within 4Å: Chain B: R.31 Ligands: FLC.10 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.31, B:R.31, B:Y.32, B:Y.32 Salt bridges: B:R.31, B:R.31

2 x LI: LITHIUM ION(Non-covalent)

LI.3: 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.3 LI.12: 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 8VN: (3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid(Non-covalent)

8VN.4: 13 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, M.196, Y.220 Ligands: 8WQ.5 14 PLIP interactions: 14 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:E.193, A:E.193 Water bridges: A:R.96, A:R.96, A:K.144, A:E.193 Salt bridges: A:R.96 pi-Stacking: A:Y.61 8VN.13: 13 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, M.196, Y.220 Ligands: 8WQ.14 14 PLIP interactions: 14 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:E.193, B:E.193 Water bridges: B:R.96, B:R.96, B:K.144, B:E.193 Salt bridges: B:R.96 pi-Stacking: B:Y.61

2 x 8WQ: (2~{S},3~{R},4~{R})-3-(carboxycarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylic acid(Non-covalent)

8WQ.5: 13 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, M.196, Y.220 Ligands: 8VN.4 11 PLIP interactions: 11 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:E.193, A:E.193 Water bridges: A:R.96, A:L.138 Salt bridges: A:R.96 8WQ.14: 13 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, M.196, Y.220 Ligands: 8VN.13 11 PLIP interactions: 11 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:E.193, B:E.193 Water bridges: B:R.96, B:L.138 Salt bridges: B:R.96

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

SO4.6: 1 residues within 4Å: Chain A: K.82 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.82 SO4.7: 2 residues within 4Å: Chain A: R.64, K.69 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.64, A:K.69 SO4.8: 2 residues within 4Å: Chain A: R.148, R.149 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.149, A:R.149, A:R.149, A:R.149 Salt bridges: A:R.149 SO4.15: 1 residues within 4Å: Chain B: K.82 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82 SO4.16: 2 residues within 4Å: Chain B: R.64, K.69 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.64, B:K.69 SO4.17: 2 residues within 4Å: Chain B: R.148, R.149 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.149, B:R.149, B:R.149, B:R.149 Salt bridges: B:R.149

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: K.60, S.140, R.172 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.60, A:S.140 Water bridges: A:Y.61, A:D.139, A:D.139, A:D.139, A:S.140 GOL.18: 3 residues within 4Å: Chain B: K.60, S.140, R.172 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.60, B:S.140 Water bridges: B:Y.61, B:D.139, B:D.139, B:D.139, B:S.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mllerud, S. et al., Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors. ACS Chem Neurosci (2017)

Release Date

2017-07-26

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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