SMTL ID : 3fvn.3 (2 other biounits)

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 9-deoxy-neodysiherbaine A in space group P1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: T.91, V.93, S.140, T.143, F.144, D.211, K.213 Chain B: E.238 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.213, B:E.238 Water bridges: A:Y.92 GOL.2: 7 residues within 4Å: Chain A: P.103, T.106, S.212, K.213, G.214 Chain B: T.106, Q.237 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:T.106, B:Q.237, A:G.214 GOL.3: 9 residues within 4Å: Chain A: F.100, K.102, R.226, T.230 Chain B: F.100, S.101, K.102, R.226, T.230 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.102, A:K.102, A:R.226, A:T.230, B:K.102, B:K.102, B:R.226, B:T.230 Water bridges: A:R.226, A:D.227, B:R.226 GOL.4: 4 residues within 4Å: Chain A: L.54, V.55, P.56, G.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.58 Water bridges: A:G.58 GOL.7: 7 residues within 4Å: Chain A: T.106, Q.237 Chain B: P.103, T.106, S.212, K.213, G.214 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.212 Water bridges: B:S.212, B:S.212, A:Q.237, A:Q.237 GOL.8: 8 residues within 4Å: Chain A: E.238 Chain B: T.91, V.93, S.140, T.143, F.144, D.211, K.213 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.91, B:K.213 Water bridges: B:Y.92, B:D.211, B:D.211, A:E.238 GOL.9: 6 residues within 4Å: Chain B: A.126, K.127, Q.128, T.129, K.155, F.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.127, B:K.155 GOL.10: 5 residues within 4Å: Chain B: R.137, D.138, M.142, K.146, W.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.137 Water bridges: B:D.138, B:K.146

2 x 9DX: (2R,3aR,7R,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-7-hydroxy-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid(Non-covalent)

9DX.5: 15 residues within 4Å: Chain A: E.12, Y.60, P.87, L.88, T.89, R.94, V.136, G.139, S.140, T.141, S.172, M.188, E.189, S.192, Y.215 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.60, A:Y.60, A:V.136 Hydrogen bonds: A:P.87, A:P.87, A:T.89, A:S.140, A:T.141, A:T.141, A:E.189, A:E.189, A:E.189 Water bridges: A:V.136 Salt bridges: A:R.94 9DX.11: 15 residues within 4Å: Chain B: E.12, Y.60, P.87, L.88, T.89, R.94, V.136, G.139, S.140, T.141, S.172, M.188, E.189, S.192, Y.215 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60, B:V.136 Hydrogen bonds: B:P.87, B:P.87, B:T.89, B:T.89, B:S.140, B:T.141, B:E.189 Water bridges: B:V.136, B:E.189 Salt bridges: B:R.94

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

SO4.6: 3 residues within 4Å: Chain A: R.30, K.53, L.54 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: A:Y.18, A:R.30, A:R.30, A:R.30, A:L.54 Salt bridges: A:R.30 SO4.12: 2 residues within 4Å: Chain B: R.3, Y.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.225, B:Y.225 Salt bridges: B:R.3 SO4.13: 4 residues within 4Å: Chain B: R.30, V.52, K.53, L.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.54 Water bridges: B:D.51, B:K.53 Salt bridges: B:R.30, B:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, M. et al., Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors. J.Mol.Biol. (2011)

Release Date

2010-01-19

Peptides

Glutamate receptor, ionotropic kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor, ionotropic kainate 1

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