SMTL ID : 6hca.1

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S1J) IN COMPLEX WITH POSITIVE ALLOSTERIC MODULATOR TDPAM02 AT 1.8 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.159 Water bridges: A:R.148 Salt bridges: A:R.148, A:R.163 SO4.2: 6 residues within 4Å: Chain A: S.108, L.109, S.194, E.198, N.214, K.251 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.108, A:S.194, A:E.198, A:N.214 Water bridges: A:S.108, A:S.108, A:K.251, A:K.251 Salt bridges: A:K.251 SO4.3: 5 residues within 4Å: Chain A: Y.61, T.91, T.93, R.96, S.142 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.91 Water bridges: A:T.91, A:R.96 Salt bridges: A:R.96 SO4.4: 2 residues within 4Å: Chain A: K.116 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.5: 3 residues within 4Å: Chain A: K.253, W.254, K.258 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.253, A:K.258 SO4.6: 4 residues within 4Å: Chain A: M.19, H.23, E.24, R.31 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.31 Salt bridges: A:H.23, A:R.31 SO4.18: 4 residues within 4Å: Chain B: D.139, S.140, K.144, R.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.139 Salt bridges: B:K.144, B:R.148 SO4.19: 7 residues within 4Å: Chain B: S.108, L.109, G.110, S.194, E.198, N.214, K.251 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.194, B:N.214, B:N.214 Water bridges: B:S.108, B:S.108, B:S.108, B:E.198, B:K.251 Salt bridges: B:K.251 SO4.20: 3 residues within 4Å: Chain B: R.148, W.159, R.163 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.159 Water bridges: B:R.163, B:R.163 Salt bridges: B:R.148, B:R.163 SO4.21: 4 residues within 4Å: Chain B: M.19, H.23, E.24, R.31 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.23, B:R.31

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 GOL.8: 8 residues within 4Å: Chain A: M.162, R.163, S.164, A.165, E.166, S.168, V.169, F.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.163, A:E.166, A:S.168 Water bridges: A:M.162, A:V.169 GOL.9: 10 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, T.208, M.209, C.261, G.262, S.263, G.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.117, A:E.201, A:E.201, A:Q.202 GOL.10: 4 residues within 4Å: Chain A: K.116, K.185, G.186 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116 Water bridges: A:K.117 GOL.11: 6 residues within 4Å: Chain A: A.124, E.125, I.152, V.154, F.155, L.215 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.124, A:E.125, A:V.154, A:G.213 GOL.12: 1 residues within 4Å: Chain A: E.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.176, A:E.176 GOL.22: 8 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, T.208, M.209, C.261, G.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.117, B:Q.202, B:C.206, B:C.261

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

CL.13: 2 residues within 4Å: Chain A: I.152, A.153 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: Q.130, T.131, E.132 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: L.26, E.27, E.30 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: E.13, S.14 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: E.27, G.28 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: I.152, A.153 Ligand excluded by PLIP

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.17: 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, N.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, N.242, L.247 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.105, A:L.247, B:P.105, B:L.247 Water bridges: A:G.219, A:N.242, A:N.242, B:G.219

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

PEG.25: 8 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, T.93, R.96, S.142, Y.220 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.89, B:T.91, B:R.96, B:R.96

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,Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2,Glutamate receptor 2

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