SMTL ID : 6hch.1 (1 other biounit)

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM01 AT 1.6 A RESOLUTION.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 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 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:T.91, A:S.142, A:S.142, A:T.143, A:T.143, E.1, E.1, E.1 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.17: 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 16 PLIP interactions: 13 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:T.91, B:T.91, B:S.142, B:S.142, B:T.143, B:T.143, E.17, E.17, E.17 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

15 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 3 residues within 4Å: Chain A: M.19, H.23 Ligands: ACT.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.23, ACT.13 ZN.3: 1 residues within 4Å: Chain A: K.210 No protein-ligand interaction detected (PLIP) ZN.4: 1 residues within 4Å: Chain A: R.203 No protein-ligand interaction detected (PLIP) ZN.5: 3 residues within 4Å: Chain A: D.156, T.160, R.163 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:D.156, H2O.2 ZN.6: 1 residues within 4Å: Chain A: E.24 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.24, A:E.24, H2O.9 ZN.7: 6 residues within 4Å: Chain A: T.9, T.54, I.55, V.56, E.77, A.83 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.54, H2O.3 ZN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.9: 2 residues within 4Å: Chain A: E.132, K.187 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.132, H2O.8 ZN.10: 2 residues within 4Å: Chain A: S.123, D.126 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, H2O.1 ZN.15: 5 residues within 4Å: Chain A: E.42, K.45, H.46, L.241 Ligands: ACT.16 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:H.46 ZN.18: 4 residues within 4Å: Chain B: E.42, K.45, H.46, L.241 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.42, B:H.46 ZN.19: 4 residues within 4Å: Chain B: D.156, W.159, T.160 Ligands: ACT.23 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.156, B:D.156, H2O.14, ACT.23 ZN.20: 1 residues within 4Å: Chain B: K.210 No protein-ligand interaction detected (PLIP) ZN.21: 1 residues within 4Å: Chain B: K.204 No protein-ligand interaction detected (PLIP) ZN.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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)

D45.11: 24 residues within 4Å: Chain A: I.92, K.104, P.105, F.106, M.107, S.108, S.217, K.218, G.219, 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, L.239, S.242, L.247 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

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

ACT.12: 6 residues within 4Å: Chain A: A.134, R.180, K.183, S.184, K.187, Y.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.188 Salt bridges: A:R.180, A:K.183 ACT.13: 5 residues within 4Å: Chain A: M.19, K.20, K.21, H.23 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.23 ACT.16: 4 residues within 4Å: Chain A: E.42, K.45, H.46 Ligands: ZN.15 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.45, A:H.46 ACT.23: 7 residues within 4Å: Chain B: R.148, R.149, S.150, K.151, D.156, W.159 Ligands: ZN.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.151 Hydrogen bonds: B:R.148 Water bridges: B:D.156 ACT.24: 5 residues within 4Å: Chain B: A.134, R.180, S.184, K.187, Y.188 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.188 Water bridges: B:R.180 Salt bridges: B:R.180

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.217 Hydrogen bonds: B:D.248, B:D.248

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

CL.25: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP

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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