SMTL ID : 3h6v.1

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5206 at 2.10 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.1, E.1, E.1 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.7: 11 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 15 PLIP interactions: 12 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, E.7, E.7, E.7 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

2 x NS6: (3R)-3-cyclopentyl-7-[(4-methylpiperazin-1-yl)sulfonyl]-3,4-dihydro-2H-1,2-benzothiazine 1,1-dioxide(Non-covalent)

NS6.2: 12 residues within 4Å: Chain A: P.105, F.106, M.107, S.108, L.239, S.242, L.247, D.248, K.251 Chain B: I.92, S.217, K.218 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.239, A:L.247, A:L.247, B:I.92, B:K.218 Hydrogen bonds: A:S.108, B:S.217 Water bridges: A:K.251, B:K.218 Salt bridges: A:D.248 NS6.8: 12 residues within 4Å: Chain A: I.92, S.217, K.218 Chain B: P.105, F.106, M.107, S.108, L.239, S.242, L.247, D.248, K.251 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.239, B:L.247, B:L.247, A:I.92, A:K.218 Hydrogen bonds: B:S.108, B:D.248, A:S.217 Salt bridges: B:D.248 Water bridges: A:K.218

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.240, A:Q.244 Water bridges: A:K.45, A:K.45 GOL.10: 5 residues within 4Å: Chain B: M.19, K.20, K.21, N.22, H.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.19, B:N.22 Water bridges: B:N.22, B:H.23

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

SO4.4: 4 residues within 4Å: Chain A: D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Water bridges: A:N.72, A:R.148, A:R.148, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.5: 3 residues within 4Å: Chain A: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.148, A:R.163 SO4.6: 2 residues within 4Å: Chain A: K.116, R.182 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.11: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:D.139, B:S.140, B:E.145, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.12: 2 residues within 4Å: Chain B: M.19, R.31 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.31, B:R.31, B:Y.32 Salt bridges: B:R.31 SO4.13: 4 residues within 4Å: Chain B: S.194, T.195, E.198, N.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.108, B:S.194, B:E.198, B:N.214 Salt bridges: B:K.251 SO4.14: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:K.45, B:K.45 Salt bridges: B:K.45, B:H.46, B:K.240

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 3 residues within 4Å: Chain B: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hald, H. et al., Distinct structural features of cyclothiazide are responsible for effects on peak current amplitude and desensitization kinetics at iGluR2. J.Mol.Biol. (2009)

Release Date

2009-07-28

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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