SMTL ID : 6hcb.1

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM01 AT 1.9 A RESOLUTION.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: M.19, E.24, R.31 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.31, A:Y.32 Salt bridges: A:R.31 SO4.2: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: PEG.13 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.140, A:S.140, A:S.140 Water bridges: A:G.141, A:K.144, A:K.144 Salt bridges: A:K.144, A:R.148 SO4.3: 5 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104, N.235 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.235, A:F.102 Water bridges: B:K.104, A:E.97, A:D.101, A:K.104 Salt bridges: B:K.104 SO4.4: 1 residues within 4Å: Chain A: P.167 No protein-ligand interaction detected (PLIP) SO4.5: 1 residues within 4Å: Chain A: S.168 No protein-ligand interaction detected (PLIP) SO4.6: 6 residues within 4Å: Chain A: M.107, S.108, D.248, K.251 Chain B: S.217 Ligands: D45.17 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.108, A:S.108, A:S.108, A:D.248, B:S.217 Water bridges: A:D.248, A:K.251, A:K.251 Salt bridges: A:K.251 SO4.14: 5 residues within 4Å: Chain A: K.104, N.235 Chain B: E.97, D.101, F.102 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.102 Water bridges: B:E.97, B:D.101, B:K.104, A:K.104 Salt bridges: A:K.104 SO4.15: 6 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 Ligands: PEG.22 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.140, B:S.140, B:S.140 Water bridges: B:G.141, B:K.144, B:K.144 Salt bridges: B:K.144, B:R.148 SO4.16: 6 residues within 4Å: Chain A: S.217 Chain B: M.107, S.108, D.248, K.251 Ligands: D45.17 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.108, B:S.108, B:S.108, B:D.248, B:D.248, A:S.217 Water bridges: B:K.251 Salt bridges: B:K.251

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.7: 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:T.143, A:T.143, E.7, E.7 Water bridges: A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.18: 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 14 PLIP interactions: 12 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.18, E.18 Water bridges: B:E.193, B:E.193 Salt bridges: B:R.96

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: S.108, L.109, G.110, S.194, T.195, E.198, K.210, N.214 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.194, A:E.198, A:K.210, A:N.214, A:N.214 Water bridges: A:N.214, A:K.251 GOL.9: 5 residues within 4Å: Chain A: S.14, M.18, R.182, Y.199, R.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.14, A:Y.199, A:R.203, A:R.203 GOL.19: 4 residues within 4Å: Chain B: D.58, K.60, N.72, G.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.72 GOL.20: 9 residues within 4Å: Chain B: S.108, L.109, G.110, S.194, T.195, E.198, K.210, N.214, K.251 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.194, B:E.198, B:E.198, B:E.198, B:E.198, B:K.210, B:N.214 Water bridges: B:K.251

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

CL.10: 3 residues within 4Å: Chain A: K.21, N.22, H.23 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: D.58, K.60, N.72 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP

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

PEG.13: 6 residues within 4Å: Chain A: K.144, R.148, W.159, R.163, F.170 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.144, A:R.148, A:R.148, A:R.163 PEG.22: 6 residues within 4Å: Chain B: K.144, R.148, W.159, R.163, F.170 Ligands: SO4.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.144, B:R.148, B:R.148, B:R.163, B:R.163

1 x D45: 6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)(Non-covalent)

D45.17: 28 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 Ligands: SO4.6, SO4.16 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.105, A:P.105 Hydrogen bonds: B:P.105, B:G.219, A:P.105, 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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