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

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.213 Water bridges: A:Y.92, A:D.211, A:D.211 GOL.2: 7 residues within 4Å: Chain A: P.103, T.106, S.212, K.213, G.214 Chain B: T.106, Q.237 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.237, A:G.214 GOL.3: 9 residues within 4Å: Chain A: I.6, T.8, K.53, L.54, V.55, P.56, E.75, R.80, A.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.8, A:L.54, A:E.75 GOL.4: 4 residues within 4Å: Chain A: D.123, I.150, T.152, Y.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.152 Water bridges: A:T.152 GOL.5: 5 residues within 4Å: Chain A: R.137, D.138, M.142, K.146, W.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.138, A:K.146 GOL.8: 7 residues within 4Å: Chain A: T.106, Q.237 Chain B: P.103, T.106, S.212, K.213, G.214 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.237, A:Q.237 Hydrogen bonds: B:S.212 GOL.9: 8 residues within 4Å: Chain A: E.238 Chain B: T.91, V.93, S.140, T.143, F.144, D.211, K.213 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.91, B:K.213 Water bridges: B:Y.92, A:E.238 GOL.10: 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

2 x 8DX: (2R,3aR,6S,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-6-hydroxy-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid(Non-covalent)

8DX.6: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.60, A:Y.60, A:V.136 Hydrogen bonds: A:P.87, A:T.89, A:T.89, A:S.140, A:T.141, A:T.141, A:E.189, A:E.189, A:E.189, A:E.189 Water bridges: A:M.142 Salt bridges: A:R.94 8DX.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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60, B:V.136 Hydrogen bonds: B:P.87, B:T.89, B:T.89, B:T.89, B:S.140, B:T.141, B:T.141, B:E.189, B:E.189, B:E.189 Water bridges: B:V.136 Salt bridges: B:R.94

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

SO4.7: 3 residues within 4Å: Chain A: R.30, K.53, L.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: 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:R.3, 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:R.30, B:D.51 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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