SMTL ID : 3h6u.1

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS1493 at 1.85 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 13 PLIP interactions: 3 Ligand-Ligand interactions, 10 interactions with chain A Hydrogen bonds: E.1, E.1, E.1, A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193 Hydrophobic interactions: A:Y.61, A:L.138 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.12: 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 13 PLIP interactions: 10 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:S.142, B:T.143, B:T.143, B:E.193, E.12, E.12, E.12 Water bridges: B:E.193 Salt bridges: B:R.96

2 x NS3: (3S)-3-cyclopentyl-6-methyl-7-[(4-methylpiperazin-1-yl)sulfonyl]-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

NS3.2: 13 residues within 4Å: Chain A: K.104, P.105, M.107, S.108, L.239, S.242, L.247, D.248, K.251 Chain B: I.92, S.217, K.218, G.219 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.104, A:L.239, A:L.247, A:D.248, B:I.92, B:K.218 Hydrogen bonds: A:S.108, A:S.242, A:S.242, B:S.217 Water bridges: A:K.251 Salt bridges: A:D.248 NS3.13: 13 residues within 4Å: Chain A: I.92, S.217, K.218, G.219 Chain B: K.104, P.105, M.107, S.108, L.239, S.242, L.247, D.248, K.251 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.104, B:L.239, B:L.247, B:D.248, A:I.92, A:K.218 Hydrogen bonds: B:S.108, B:S.242, B:S.242, A:S.217 Water bridges: B:K.251 Salt bridges: B:D.248

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

SO4.3: 4 residues within 4Å: Chain A: E.24, L.26, E.27, R.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.27 Water bridges: A:E.27, A:R.31, A:R.31, A:R.31 Salt bridges: A:R.31 SO4.4: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.139, A:S.140 Water bridges: A:N.72, A:K.144, A:K.144, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.5: 2 residues within 4Å: Chain A: R.149 Ligands: FLC.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.148 Salt bridges: A:R.149 SO4.6: 3 residues within 4Å: Chain A: N.22, L.26, E.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22 SO4.7: 1 residues within 4Å: Chain A: K.116 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.8: 5 residues within 4Å: Chain A: L.109, S.194, E.198, N.214, K.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.194, A:E.198 Water bridges: A:N.214 Salt bridges: A:K.251 SO4.14: 4 residues within 4Å: Chain B: E.24, L.26, E.27, R.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.27 Water bridges: B:E.27, B:R.31, B:R.31, B:R.31 Salt bridges: B:R.31 SO4.15: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.139, B:S.140 Water bridges: B:N.72, B:K.144, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.16: 2 residues within 4Å: Chain B: R.149 Ligands: FLC.22 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.148 Salt bridges: B:R.149 SO4.17: 3 residues within 4Å: Chain B: N.22, L.26, E.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22 SO4.18: 1 residues within 4Å: Chain B: K.116 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.116, B:K.116 Salt bridges: B:K.116 SO4.19: 5 residues within 4Å: Chain B: L.109, S.194, E.198, N.214, K.251 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.194, B:E.198 Water bridges: B:N.214 Salt bridges: B:K.251

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: E.33, W.254, K.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.33, A:K.258 GOL.10: 5 residues within 4Å: Chain A: E.42, K.45, H.46, L.241, Q.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.42, A:K.45, A:H.46, A:Q.244 GOL.20: 3 residues within 4Å: Chain B: E.33, W.254, K.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.33, B:K.258 GOL.21: 5 residues within 4Å: Chain B: E.42, K.45, H.46, L.241, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.42, B:K.45, B:H.46, B:Q.244

2 x FLC: CITRATE ANION(Non-covalent)

FLC.11: 5 residues within 4Å: Chain A: R.148, R.149, W.159, R.163 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.148, A:R.149, A:R.163 FLC.22: 5 residues within 4Å: Chain B: R.148, R.149, W.159, R.163 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.148, B:R.149, 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
A

Glutamate receptor 2

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