SMTL ID : 3fas.1

X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-glutamate at 1.40A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.59, P.87, L.88, T.89, R.94, L.136, G.139, S.140, T.141, E.191, Y.218 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.59, A:L.136 Hydrogen bonds: A:P.87, A:T.89, A:S.140, A:T.141, A:T.141, A:E.191, E.1, E.1, E.1 Water bridges: A:E.191 Salt bridges: A:R.94 GLU.9: 11 residues within 4Å: Chain B: Y.59, P.87, L.88, T.89, R.94, L.136, G.139, S.140, T.141, E.191, Y.218 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.59, B:L.136 Hydrogen bonds: B:P.87, B:T.89, B:T.89, B:T.89, B:S.140, B:T.141, B:T.141, E.9, E.9, E.9 Water bridges: B:E.191 Salt bridges: B:R.94

8 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.138 Water bridges: A:S.138, A:K.142, A:K.142, A:E.143, A:R.146, A:R.146 Salt bridges: A:K.142, A:R.146 SO4.3: 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 SO4.4: 7 residues within 4Å: Chain A: E.95, D.99, F.100, K.224, R.229 Chain B: K.102, N.233 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.95, A:D.99, A:F.100 Water bridges: A:R.229, A:R.229, A:R.229, A:R.229, B:R.229, B:N.233, B:N.233 Salt bridges: A:K.224, A:R.229, B:K.102 SO4.10: 5 residues within 4Å: Chain B: A.61, D.137, S.138, K.142, R.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.138, B:S.138 Water bridges: B:R.146 Salt bridges: B:K.142, B:R.146 SO4.11: 2 residues within 4Å: Chain B: H.44, K.238 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.238 SO4.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.13: 6 residues within 4Å: Chain A: K.102, N.233 Chain B: E.95, D.99, F.100, R.229 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Water bridges: A:R.229, A:N.233, A:N.233, B:R.229, B:R.229 Salt bridges: A:K.102, B:K.224, B:R.229 Hydrogen bonds: B:D.99, B:F.100, B:F.100 SO4.14: 4 residues within 4Å: Chain B: Y.17, H.21, E.22, K.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.17 Salt bridges: B:H.21, B:K.29

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.146, W.157, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.146, A:R.146, A:R.161 GOL.6: 5 residues within 4Å: Chain A: N.212, L.213, D.214, S.215 Chain B: D.246 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:D.246, A:S.215, A:S.215, A:S.215 Hydrogen bonds: A:D.214 GOL.7: 4 residues within 4Å: Chain A: Y.17, H.21, E.22, K.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.21, A:K.29 Water bridges: A:Y.17, A:Y.30 GOL.8: 4 residues within 4Å: Chain A: E.123, I.150, V.152, Y.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.123, A:Y.153 Water bridges: A:V.152, A:Y.153 GOL.15: 5 residues within 4Å: Chain A: D.246 Chain B: N.212, L.213, D.214, S.215 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.213, A:D.246 Water bridges: B:S.215, B:S.215 GOL.16: 3 residues within 4Å: Chain B: R.146, W.157, R.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.146, B:R.161, B:R.161 Water bridges: B:W.157 GOL.17: 4 residues within 4Å: Chain B: E.25, G.26, K.29, K.50 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.25, B:E.25, B:G.26, B:Y.30, B:K.50, B:K.50 GOL.18: 3 residues within 4Å: Chain B: W.69, V.77, V.97 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.62, B:K.67, B:W.69, B:Y.78 GOL.19: 7 residues within 4Å: Chain B: E.40, K.43, H.44, K.238, L.239, A.242, V.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.40, B:K.43, B:K.238

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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