SMTL ID : 6hc9.1

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 2.4 A RESOLUTION.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: G.62, A.63, R.64, W.71, V.75, T.93, V.95, R.96, G.141, S.142, E.145, R.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.64, A:T.93, A:T.93, A:R.96, A:R.96, A:E.145 Water bridges: A:V.95

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

CL.2: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: G.28, N.29 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: K.21, N.22, H.23 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: E.243 Chain B: T.93, Y.94 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: N.29, K.50, Y.51 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: L.12, M.18, M.19 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: I.152, A.153 Ligand excluded by PLIP

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 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: 2 Ligand-Ligand interactions, 13 interactions with chain A Hydrogen bonds: E.3, E.3, A:T.91, A:T.91, A:S.142, A:S.142, A:T.143, A:T.143, A:E.193, A:E.193 Hydrophobic interactions: A:Y.61, A:L.138 Water bridges: A:L.138, A:K.144 Salt bridges: A:R.96 GLU.16: 14 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, K.144, L.192, E.193, M.196, Y.220 16 PLIP interactions: 14 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:S.142, B:T.143, B:T.143, B:Y.220, E.16, E.16 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

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

SO4.4: 7 residues within 4Å: Chain A: A.63, D.139, S.140, G.141, K.144, R.148 Ligands: PGE.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.140, A:S.140, A:S.140 Salt bridges: A:K.144, A:R.148 SO4.5: 4 residues within 4Å: Chain A: H.46, K.240, Q.244 Chain B: K.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.244 Salt bridges: A:H.46, A:K.240 SO4.6: 4 residues within 4Å: Chain A: M.19, H.23, E.24, R.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.23, A:R.31 Salt bridges: A:H.23 SO4.17: 6 residues within 4Å: Chain B: A.63, D.139, S.140, G.141, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.140, B:S.140, B:S.140 Salt bridges: B:K.144, B:R.148 SO4.18: 3 residues within 4Å: Chain B: M.19, H.23, R.31 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.32 Salt bridges: B:R.31 SO4.19: 5 residues within 4Å: Chain A: K.151 Chain B: K.45, H.46, K.240, Q.244 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:H.46, B:H.46, B:K.240 Salt bridges: B:H.46 SO4.20: 3 residues within 4Å: Chain A: K.240 Chain B: Y.94, R.149 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.240, B:R.149 SO4.21: 3 residues within 4Å: Chain B: R.148, W.159, R.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.159 Salt bridges: B:R.148, B:R.163

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

PEG.7: 7 residues within 4Å: Chain A: K.116, K.117, G.118, T.119, P.120, K.185, G.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116, A:G.118 PEG.8: 10 residues within 4Å: Chain A: I.11, L.12, E.13, I.55, V.56, G.59, Y.61, L.138, T.173, T.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.12, A:T.174, A:T.174 PEG.23: 6 residues within 4Å: Chain B: S.123, A.124, E.125, I.152, V.154, F.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.123, B:A.124, B:E.125

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 7 residues within 4Å: Chain A: K.144, R.148, R.149, W.159, R.163, F.170 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.144, A:R.148, A:W.159, A:R.163, A:R.163

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.22: 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, A:L.247 Hydrogen bonds: B:G.219, A:G.219

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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