SMTL ID : 3h6t.1 (1 other biounit)

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and cyclothiazide at 2.25 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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 15 PLIP interactions: 12 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:T.91, A:S.142, A:T.143, A:T.143, E.1, E.1, E.1 Water bridges: A:K.144, A:E.193 Salt bridges: A:R.96 GLU.10: 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.10, E.10, E.10 Water bridges: B:K.144, B:E.193 Salt bridges: B:R.96

2 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 14 residues within 4Å: Chain A: K.104, 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, G.219 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:K.104, A:L.239, A:L.247, B:I.92, B:K.218 Hydrogen bonds: A:S.108, A:S.242, A:S.242, B:S.217, B:S.217 Water bridges: A:S.108, B:K.218 CYZ.11: 15 residues within 4Å: Chain A: I.92, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247, D.248, K.251 Ligands: GOL.7 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:K.104, B:K.104, B:L.239, B:L.247, A:I.92, A:K.218 Hydrogen bonds: B:S.108, B:S.242, B:S.242, A:S.217, A:S.217 Water bridges: B:S.108, B:S.108, A:K.218

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: E.42, H.46 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:H.46 ZN.4: 2 residues within 4Å: Chain A: H.23 Ligands: ACT.8 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.23, ACT.8, H2O.11 ZN.5: 2 residues within 4Å: Chain A: E.122, D.126 No protein-ligand interaction detected (PLIP) ZN.12: 3 residues within 4Å: Chain B: E.42, K.45, H.46 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.16, H2O.16 ZN.13: 1 residues within 4Å: Chain B: D.156 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.156, H2O.20

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: E.24 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 Ligands: CYZ.11 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.242, B:D.248, B:D.248, A:N.214 Water bridges: B:G.245, A:S.217 GOL.14: 2 residues within 4Å: Chain B: Y.80, K.82 No protein-ligand interaction detected (PLIP) GOL.15: 3 residues within 4Å: Chain B: K.4, G.81, D.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.4, B:K.4, B:G.81 GOL.16: 7 residues within 4Å: Chain B: K.116, K.117, G.118, T.119, P.120, K.185, G.186 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.116, B:K.116, B:K.185, B:K.187, B:K.187 GOL.17: 4 residues within 4Å: Chain A: L.236 Chain B: E.97, E.98, K.226 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.232, B:K.226, B:K.226

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: M.19, H.23 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.23 ACT.18: 2 residues within 4Å: Chain B: E.201, K.210 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.210

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

DMS.9: 2 residues within 4Å: Chain A: E.201, K.210 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.201

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
C

Glutamate receptor 2

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