SMTL ID : 5ns9.1

Crystal structure of the GluA2 LBD (L483Y-N754S-L758V) in complex with glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 10 residues within 4Å: Chain A: K.145, E.229, Q.230, T.236, M.237, K.238, Y.284, C.289, G.290, S.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.145, A:Q.230 1PE.2: 8 residues within 4Å: Chain A: K.32, V.34, G.76, F.77, D.112, S.256, S.257, L.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.257

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 6 residues within 4Å: Chain A: K.32, V.35, G.109, K.110, A.111, D.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.32

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

SO4.4: 1 residues within 4Å: Chain A: R.177 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.177 Salt bridges: A:R.177 SO4.5: 4 residues within 4Å: Chain A: K.49, R.231, K.232, E.288 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.231, A:R.231 Salt bridges: A:K.49, A:R.231, A:K.232 SO4.6: 3 residues within 4Å: Chain A: R.176, W.187, R.191 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.176, A:W.187, A:R.191 Salt bridges: A:R.176, A:R.191 SO4.7: 5 residues within 4Å: Chain A: A.91, D.167, S.168, K.172, R.176 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.168 Water bridges: A:K.172, A:K.172, A:R.176, A:R.176 Salt bridges: A:K.172, A:R.176 SO4.12: 3 residues within 4Å: Chain B: M.47, R.59, Y.60 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.59, B:R.59, B:R.59, B:R.59, B:Y.60 Salt bridges: B:R.59 SO4.13: 5 residues within 4Å: Chain B: A.91, D.167, S.168, K.172, R.176 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.168 Water bridges: B:A.91, B:N.100, B:S.168, B:K.172, B:K.172, B:R.176, B:R.176 Salt bridges: B:K.172, B:R.176

5 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: E.125, I.128, D.129, K.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.125, A:E.125 Water bridges: A:F.130, A:K.254, A:G.255 NA.9: 4 residues within 4Å: Chain A: R.177, S.178 Chain B: E.271, Q.272 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:K.179 Hydrogen bonds: B:E.271 NA.10: 6 residues within 4Å: Chain A: I.180, F.183, L.243, D.244 Chain B: G.273, D.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.276, B:D.276 NA.14: 6 residues within 4Å: Chain B: T.37, T.38, T.82, I.83, V.84, E.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.82, B:E.105 NA.15: 6 residues within 4Å: Chain B: S.140, I.141, V.239, G.240, G.241, L.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.141, B:G.241

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.11: 13 residues within 4Å: Chain A: Y.89, P.117, L.118, T.119, R.124, L.166, G.169, S.170, T.171, L.220, E.221, M.224, Y.248 15 PLIP interactions: 11 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.89, A:L.166 Hydrogen bonds: A:P.117, A:T.119, A:T.119, A:S.170, A:T.171, A:T.171, E.11, E.11, E.11, E.11 Water bridges: A:L.166, A:E.221 Salt bridges: A:R.124 GLU.16: 14 residues within 4Å: Chain B: Y.89, P.117, L.118, T.119, R.124, L.166, G.169, S.170, T.171, K.172, L.220, E.221, M.224, Y.248 15 PLIP interactions: 11 interactions with chain B, 4 Ligand-Ligand interactions Hydrophobic interactions: B:Y.89, B:L.166 Hydrogen bonds: B:P.117, B:T.119, B:T.119, B:S.170, B:T.171, B:T.171, E.16, E.16, E.16, E.16 Water bridges: B:L.166, B:E.221 Salt bridges: B:R.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Unitary Properties of AMPA Receptors with Reduced Desensitization. Biophys. J. (2017)

Release Date

2017-09-13

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