SMTL ID : 3tdj.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and BPAM-97 at 1.95 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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:T.91, A:S.142, A:T.143, A:T.143 Hydrophobic interactions: A:Y.61, A:L.138 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.14: 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 12 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, E.14, E.14 Water bridges: B:E.193, B:E.193 Salt bridges: B:R.96

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

SO4.2: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:G.141 Salt bridges: A:K.144, A:R.148 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:D.139, B:S.140 Water bridges: B:K.144, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.22: 3 residues within 4Å: Chain B: N.3, K.4, T.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.5, B:T.5

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: R.163 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: A.153 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.116, K.117, T.119, G.186 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: K.50, Y.51 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: K.116 Ligands: GOL.21 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.240, Q.244 Chain B: K.151 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.244 GOL.6: 5 residues within 4Å: Chain A: K.240, E.243, Q.244 Chain B: R.149 Ligands: GOL.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:Y.94, B:Y.94, B:K.151 Hydrogen bonds: A:K.240, A:E.243, A:E.243 GOL.7: 3 residues within 4Å: Chain A: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 GOL.8: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.214, A:D.248 Water bridges: B:S.217 GOL.9: 3 residues within 4Å: Chain A: M.19, H.23, R.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.23, A:H.23 Water bridges: A:R.31 GOL.16: 3 residues within 4Å: Chain B: R.148, W.159, R.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.148, B:R.163, B:R.163 GOL.17: 6 residues within 4Å: Chain B: G.62, A.63, W.71, T.93, R.96, E.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.93, B:R.96 Water bridges: B:R.64, B:E.145 GOL.18: 5 residues within 4Å: Chain B: S.108, S.194, E.198, K.210, N.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.194, B:E.198, B:E.198, B:N.214 Water bridges: B:K.251 GOL.19: 4 residues within 4Å: Chain B: M.19, H.23, E.24, R.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.23, B:H.23, B:R.31 GOL.20: 4 residues within 4Å: Chain B: E.27, G.28, R.31, K.52 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.28, B:R.31, B:R.31, B:K.52 GOL.21: 4 residues within 4Å: Chain B: K.116, K.185, G.186 Ligands: CL.23 No protein-ligand interaction detected (PLIP)

2 x 3TJ: 4-ethyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

3TJ.12: 15 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Chain B: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Ligands: 3TJ.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.105 Hydrogen bonds: B:G.219 Halogen bonds: B:M.107 3TJ.13: 15 residues within 4Å: Chain A: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Ligands: 3TJ.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.105 Hydrogen bonds: A:G.219 Halogen bonds: A:M.107

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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