SMTL ID : 3fv2.3 (2 other biounits)

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 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: 2 residues within 4Å: Chain A: R.170, E.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:E.174 GOL.2: 6 residues within 4Å: Chain A: A.126, K.127, Q.128, T.129, K.155, F.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.127, A:K.155 GOL.3: 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 A, 1 interactions with chain B Hydrogen bonds: A:S.212 Water bridges: A:G.214, B:Q.237 GOL.4: 8 residues within 4Å: Chain A: T.91, V.93, S.140, T.143, F.144, D.211, K.213 Chain B: E.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.213 Water bridges: A:Y.92 GOL.5: 9 residues within 4Å: Chain A: I.6, T.8, K.53, L.54, V.55, P.56, E.75, R.80, A.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.8, A:L.54, A:E.75 Water bridges: A:R.80 GOL.6: 4 residues within 4Å: Chain A: D.123, I.150, T.152, Y.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.152 Water bridges: A:T.152, A:Y.153 GOL.7: 6 residues within 4Å: Chain A: R.137, D.138, M.142, K.146, W.157, L.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.137, A:D.138, A:K.146 GOL.11: 8 residues within 4Å: Chain B: A.126, K.127, Q.128, T.129, I.131, Y.133, K.155, F.159 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.128, B:I.131, B:Y.133, B:Y.133 Water bridges: B:A.126, B:K.127 GOL.12: 7 residues within 4Å: Chain A: T.106, Q.237 Chain B: P.103, T.106, S.212, K.213, G.214 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:T.106, A:Q.237, A:Q.237 Hydrogen bonds: B:S.212 GOL.13: 9 residues within 4Å: Chain A: F.100, K.102, R.226, T.230 Chain B: F.100, K.102, R.226, D.227, T.230 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.102, A:K.102, A:R.226, A:T.230, A:T.230, B:R.226, B:D.227 Water bridges: A:R.226, A:D.227

2 x NDZ: (2R,3aR,6R,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6,7-dihydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid(Non-covalent)

NDZ.8: 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:T.89, A:T.89, A:S.140, A:T.141, A:T.141, A:E.189, A:E.189, A:S.192 Water bridges: A:V.136, A:S.192 Salt bridges: A:R.94 NDZ.14: 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60, B:V.136 Hydrogen bonds: B:T.89, B:T.89, B:T.89, B:S.140, B:T.141, B:T.141, B:E.189, B:S.192, B:Y.215 Water bridges: B:V.136 Salt bridges: B:R.94

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

SO4.9: 4 residues within 4Å: Chain A: R.30, V.52, K.53, L.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: A:R.30 Salt bridges: A:R.30, A:K.53 SO4.10: 1 residues within 4Å: Chain A: K.248 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.19, A:R.19, A:K.248, A:K.248 Salt bridges: A:K.40, A:K.248 SO4.15: 3 residues within 4Å: Chain B: R.30, K.53, L.54 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.54 Water bridges: B:R.30, B:R.30 Salt bridges: B:R.30

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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