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

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: E.12, E.13, P.14, S.172, D.173, I.176, M.188, S.192, Y.195, V.196 Ligands: 8EP.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.12, A:S.172, A:D.173, A:S.192, A:S.192 GOL.2: 7 residues within 4Å: Chain A: P.103, T.106, S.212, K.213, G.214 Chain B: T.106, Q.237 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.212 Water bridges: A:G.214, B:T.106, B:Q.237 GOL.3: 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: 3 interactions with chain A Hydrogen bonds: A:K.213 Water bridges: A:Y.92, A:D.211 GOL.4: 4 residues within 4Å: Chain A: L.54, V.55, P.56, G.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.58 GOL.8: 9 residues within 4Å: Chain A: E.238 Chain B: T.89, 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: 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.10: 9 residues within 4Å: Chain B: E.12, E.13, P.14, S.172, I.176, S.192, Y.195, V.196 Ligands: 8EP.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.172, B:S.192, B:S.192, B:S.192 Water bridges: B:E.13 GOL.11: 2 residues within 4Å: Chain B: K.40, Y.50 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.28, B:N.28, B:N.28, B:Y.50 GOL.12: 6 residues within 4Å: Chain B: R.137, D.138, M.142, K.146, W.157, L.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.137, B:R.137 Water bridges: B:D.138 GOL.13: 8 residues within 4Å: Chain B: T.8, K.53, L.54, V.55, P.56, E.75, R.80, A.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.8, B:K.53, B:L.54, B:R.80

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

8EP.5: 16 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 Ligands: GOL.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.60, A:Y.60, A:V.136 Hydrogen bonds: A:E.12, 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, A:E.189, A:S.192 Water bridges: A:V.136 Salt bridges: A:R.94 8EP.14: 16 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 Ligands: GOL.10 16 PLIP interactions: 16 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:T.141, B:E.189, B:E.189, B:E.189, B:S.192 Water bridges: B:V.136 Salt bridges: B:R.94

4 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 SO4.7: 2 residues within 4Å: Chain A: R.3, Y.225 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.3 SO4.15: 4 residues within 4Å: Chain B: R.30, V.52, K.53, L.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.54 Water bridges: B:R.30 Salt bridges: B:R.30 SO4.16: 3 residues within 4Å: Chain B: R.3, L.5, Y.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.225, B:Y.225 Salt bridges: B:R.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, M. et al., Crystal Structures of Human GluR5 Ligand-Binding Core in Complexes with Novel Marine-Derived Toxins, Dysiherbaine and Neodysiherbaine A, and Their Analogues. To be Published

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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