SMTL ID : 3fat.1 (1 other biounit)

X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x AMQ: (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID(Non-covalent)

AMQ.1: 13 residues within 4Å: Chain A: Y.59, P.87, L.88, T.89, R.94, L.136, G.139, S.140, T.141, L.190, E.191, M.194, Y.218 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.59, A:Y.59, A:L.136 Hydrogen bonds: A:P.87, A:T.89, A:T.89, A:S.140, A:T.141, A:E.191, A:E.191 Water bridges: A:T.141, A:T.141, A:L.189 Salt bridges: A:R.94 AMQ.8: 13 residues within 4Å: Chain B: Y.59, P.87, L.88, T.89, R.94, L.136, G.139, S.140, T.141, L.190, E.191, M.194, Y.218 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.59, B:L.136 Hydrogen bonds: B:P.87, B:T.89, B:T.89, B:S.140, B:S.140, B:T.141, B:E.191 Water bridges: B:T.141, B:T.141, B:T.141, B:L.189 Salt bridges: B:R.94

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

SO4.2: 5 residues within 4Å: Chain A: A.61, D.137, S.138, K.142, R.146 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.138 Water bridges: A:D.137, A:S.138, A:G.139, A:E.143 Salt bridges: A:K.142, A:R.146 SO4.3: 3 residues within 4Å: Chain A: R.146, W.157, R.161 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.146, A:W.157 Salt bridges: A:R.146, A:R.161 SO4.4: 2 residues within 4Å: Chain A: H.44, K.238 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.238, A:K.238 Salt bridges: A:H.44, A:K.238 SO4.5: 2 residues within 4Å: Chain A: G.1, R.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.2 Salt bridges: A:R.2 SO4.9: 1 residues within 4Å: Chain B: R.2 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.2

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.226, S.227, R.229, T.230, P.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.230 Water bridges: A:R.229, A:T.230 GOL.10: 8 residues within 4Å: Chain A: P.103, F.104, M.105, S.106, S.240 Chain B: S.215, K.216 Ligands: GOL.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.105, A:S.240, A:S.240, B:S.215 GOL.11: 8 residues within 4Å: Chain A: S.215, K.216 Chain B: P.103, F.104, S.106, S.240, L.245 Ligands: ACY.15 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:F.104, B:S.240 Water bridges: B:S.106, B:S.106, B:S.106, A:S.106, A:S.106, A:K.216, A:K.216 GOL.12: 8 residues within 4Å: Chain A: S.240, E.241, D.246 Chain B: F.144, D.214, S.215, K.216 Ligands: GOL.10 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.147, B:D.214, B:D.214, B:S.215, A:D.246 GOL.13: 7 residues within 4Å: Chain B: I.113, K.115, G.116, T.117, I.119, E.120, M.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.116, B:T.117, B:E.120

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 3 residues within 4Å: Chain A: M.105, S.106 Chain B: S.215 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.106, B:S.215 Water bridges: A:D.246 ACY.14: 7 residues within 4Å: Chain B: A.132, Y.159, E.164, P.165, S.166, V.167, R.178 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.132 Hydrogen bonds: B:P.165 Salt bridges: B:R.178 ACY.15: 5 residues within 4Å: Chain A: S.215 Chain B: M.105, S.106, D.246 Ligands: GOL.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.246 Hydrogen bonds: A:S.215 ACY.16: 3 residues within 4Å: Chain B: H.21, E.22, K.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.22 Salt bridges: B:H.21, B:K.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasper, C. et al., Molecular mechanism of agonist recognition by the ligand-binding core of the ionotropic glutamate receptor 4. Febs Lett. (2008)

Release Date

2008-12-09

Peptides

Glutamate receptor 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 4

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