SMTL ID : 3tkd.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and cyclothiazide at 1.45 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 13 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, L.192, E.193, M.196, 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:S.142, A:S.142, A:T.143, A:T.143, A:E.193, E.1, E.1, E.1 Water bridges: A:L.138, A:E.193 Salt bridges: A:R.96 GLU.7: 14 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:S.142, B:S.142, B:T.143, B:T.143, B:E.193, E.7 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

2 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.2: 17 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, V.238, L.239, S.242, L.247, D.248, K.251 Chain B: I.92, T.93, P.105, S.217, K.218, G.219 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.104, A:L.239, A:L.247, B:I.92, B:I.92 Hydrogen bonds: A:P.105, A:S.108, A:S.108, A:S.242, B:S.217 Water bridges: B:K.218 CYZ.8: 17 residues within 4Å: Chain A: I.92, T.93, P.105, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, V.238, L.239, S.242, L.247, D.248, K.251 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:K.104, B:L.239, B:L.247, A:I.92, A:I.92, A:K.218 Hydrogen bonds: B:P.105, B:S.108, B:S.108, B:S.242, A:S.217 Water bridges: B:K.251, B:K.251, A:K.218

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

SO4.3: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Water bridges: A:A.63, A:N.72, A:S.140, A:K.144, A:K.144, A:E.145, A:R.148, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.4: 1 residues within 4Å: Chain A: K.82 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.82 SO4.5: 4 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Water bridges: B:K.104, B:N.235, B:N.235, B:N.235, A:E.97, A:E.97 Salt bridges: B:K.104 Hydrogen bonds: A:E.97, A:F.102, A:F.102 SO4.6: 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 SO4.9: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 Water bridges: B:K.144, B:K.144, B:E.145, B:R.148, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.10: 3 residues within 4Å: Chain B: M.19, R.31, Y.32 6 PLIP interactions: 6 interactions with chain B Water bridges: B:H.23, B:H.23, B:R.31, B:R.31, B:Y.32 Salt bridges: B:R.31 SO4.11: 5 residues within 4Å: Chain A: K.104, N.235 Chain B: E.97, D.101, F.102 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.97, B:F.102, B:F.102 Water bridges: B:E.97, B:E.97, A:K.104, A:N.235 Salt bridges: A:K.104 SO4.12: 3 residues within 4Å: Chain A: K.151 Chain B: K.240, Q.244 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.244 Salt bridges: B:K.240, A:K.151

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain B: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.148, B:R.148, B:W.159, B:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krintel, C. et al., Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2. Biochem.J. (2012)

Release Date

2011-09-21

Peptides

GLUTAMATE RECEPTOR 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GLUTAMATE RECEPTOR 2

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