SMTL ID : 6hcc.1

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 1.6 A RESOLUTION.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

1 x FXW: 6,6'-(ETHANE-1,2-DIYL)BIS(4-CYCLOPROPYL-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE)(Non-covalent)

FXW.1: 26 residues within 4Å: Chain A: I.92, K.104, P.105, F.106, M.107, S.108, S.217, K.218, G.219, V.238, L.239, S.242, L.247 Chain B: I.92, K.104, P.105, F.106, M.107, S.108, S.217, K.218, G.219, V.238, L.239, S.242, L.247 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.105, B:L.247, A:P.105 Hydrogen bonds: B:G.219, A:P.105, A:G.219

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 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 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:S.142, A:T.143, A:T.143, E.2, E.2 Water bridges: A:E.193, A:E.193 Salt bridges: A:R.96 GLU.16: 13 residues within 4Å: Chain B: 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: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:T.91, B:S.142, B:S.142, B:T.143, B:T.143, E.16, E.16 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

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

SO4.3: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: ACT.14 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.140, A:S.140, A:S.140 Water bridges: A:N.72, A:K.144, A:K.144, A:R.148, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.4: 3 residues within 4Å: Chain A: K.116, K.185 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.17: 2 residues within 4Å: Chain B: M.19, R.31 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 SO4.18: 4 residues within 4Å: Chain B: K.45, H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:H.46, B:H.46 Salt bridges: B:H.46 SO4.19: 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, B:S.140 Water bridges: B:K.144, B:K.144, B:R.148, B:R.148 Salt bridges: B:K.144, B:R.148

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: R.148, W.159, R.163 Ligands: ACT.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:W.159, A:R.163 GOL.6: 4 residues within 4Å: Chain A: M.19, H.23, E.24, R.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.23, A:R.31 GOL.7: 4 residues within 4Å: Chain A: H.46, K.240, Q.244 Chain B: K.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.240, A:Q.244 GOL.8: 5 residues within 4Å: Chain A: K.116, K.117, K.185, G.186 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 GOL.9: 3 residues within 4Å: Chain A: N.3, K.4, T.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.5 Water bridges: A:N.3, A:N.3, A:T.5 GOL.20: 5 residues within 4Å: Chain B: E.27, G.28, N.29, E.30, K.52 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.27, B:N.29, B:E.30 Water bridges: B:E.27, B:N.29, B:N.29 GOL.21: 5 residues within 4Å: Chain B: V.7, G.81, K.82, A.83, D.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.81

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 5 residues within 4Å: Chain A: E.27, G.28, R.31, K.52, T.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.28, A:K.52 Water bridges: A:Y.32, A:T.54 PEG.22: 3 residues within 4Å: Chain B: R.148, W.159, R.163 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.148, B:R.148, B:W.159, B:R.163, B:R.163

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

CL.11: 2 residues within 4Å: Chain A: K.50, Y.51 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: K.21, N.22, H.23 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: I.152, A.153 Ligand excluded by PLIP

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

ACT.12: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.214 Water bridges: B:S.217 ACT.13: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.214 Water bridges: A:S.217 ACT.14: 7 residues within 4Å: Chain A: K.144, R.148, W.159, R.163, F.170 Ligands: SO4.3, GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.163, A:F.170 Hydrogen bonds: A:R.148 Salt bridges: A:K.144 ACT.15: 5 residues within 4Å: Chain A: E.97, D.101, F.102, S.103 Chain B: K.104 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:N.235, A:D.101, A:D.101 Salt bridges: B:K.104 Hydrophobic interactions: A:D.101 Hydrogen bonds: A:F.102, A:F.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laulumaa, S. et al., Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor. Acs Med.Chem.Lett. (2019)

Release Date

2019-04-03

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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