SMTL ID : 3rn8.2 (1 other biounit)

Crystal Structure of iGluR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.62, P.90, L.91, T.92, R.97, L.139, G.142, S.143, T.144, E.194, Y.221 14 PLIP interactions: 3 Ligand-Ligand interactions, 11 interactions with chain A Hydrogen bonds: E.1, E.1, E.1, A:P.90, A:T.92, A:S.143, A:T.144, A:T.144, A:E.194 Hydrophobic interactions: A:Y.62, A:L.139 Water bridges: A:L.139, A:E.194 Salt bridges: A:R.97 GLU.8: 11 residues within 4Å: Chain B: Y.62, P.90, L.91, T.92, R.97, L.139, G.142, S.143, T.144, E.194, Y.221 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.62, B:L.139 Hydrogen bonds: B:P.90, B:T.92, B:S.143, B:T.144, B:T.144, B:E.194, E.8, E.8, E.8 Water bridges: B:L.139, B:E.194 Salt bridges: B:R.97

2 x RN8: 3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid)(Non-covalent)

RN8.2: 20 residues within 4Å: Chain A: I.93, P.106, M.108, S.109, S.218, K.219, G.220, V.239, N.243 Chain B: I.93, P.106, F.107, M.108, S.109, S.218, K.219, G.220, L.240, N.243 Ligands: RN8.9 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.106, A:V.239, A:N.243, B:P.106, B:L.240 Hydrogen bonds: A:S.109, B:S.109 Water bridges: A:I.93, A:S.218, B:I.93 RN8.9: 20 residues within 4Å: Chain A: I.93, P.106, F.107, M.108, S.109, S.218, K.219, G.220, L.240, N.243 Chain B: I.93, P.106, M.108, S.109, S.218, K.219, G.220, V.239, N.243 Ligands: RN8.2 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.106, B:V.239, B:N.243, A:P.106, A:L.240 Hydrogen bonds: B:S.109, A:S.109 Water bridges: B:I.93, B:S.218, A:I.93

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: E.167 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.167, A:E.167 ZN.4: 2 residues within 4Å: Chain A: H.24, E.31 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.24, A:E.31, A:E.31, H2O.11 ZN.5: 5 residues within 4Å: Chain A: E.43, K.46, H.47, L.242, Q.245 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.43, A:H.47, H2O.9 ZN.10: 2 residues within 4Å: Chain B: E.167 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.167, B:E.167 ZN.11: 2 residues within 4Å: Chain B: H.24, E.31 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.24, B:E.31, B:E.31, H2O.24 ZN.12: 5 residues within 4Å: Chain B: E.43, K.46, H.47, L.242, Q.245 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.43, B:H.47, H2O.22

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

ACT.6: 5 residues within 4Å: Chain A: A.135, R.181, S.185, K.188, Y.189 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.135 Hydrogen bonds: A:S.185, A:S.185 Water bridges: A:R.181, A:R.181 Salt bridges: A:R.181 ACT.13: 5 residues within 4Å: Chain B: A.135, R.181, S.185, K.188, Y.189 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.135 Hydrogen bonds: B:S.185, B:S.185 Water bridges: B:R.181, B:R.181 Salt bridges: B:R.181

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

SO4.7: 6 residues within 4Å: Chain A: R.164, A.166, E.167, S.169, F.171 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.169 Water bridges: A:A.166, A:S.169, A:S.169, A:V.170 SO4.14: 6 residues within 4Å: Chain B: R.164, A.166, E.167, S.169, F.171 Ligands: ZN.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.169 Water bridges: B:A.166, B:S.169, B:S.169, B:V.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timm, D.E. et al., Structural and functional analysis of two new positive allosteric modulators of GluA2 desensitization and deactivation. Mol.Pharmacol. (2011)

Release Date

2011-05-25

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Glutamate receptor 2

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