SMTL ID : 4n07.2 (1 other biounit)

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and BPAM-344 at 1.87 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.1: 16 residues within 4Å: Chain A: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Ligands: 2J9.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.105, B:L.247 Hydrogen bonds: A:G.219 Halogen bonds: A:M.107 2J9.10: 16 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Chain B: I.92, P.105, M.107, S.108, S.217, K.218, G.219 Ligands: 2J9.1 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.247, B:P.105 Hydrogen bonds: B:G.219 Halogen bonds: B:M.107

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 11 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, 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:T.91, 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.11: 11 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, 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:T.143, B:T.143, E.11, E.11 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

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

ACT.3: 3 residues within 4Å: Chain A: M.19, H.23 Ligands: ZN.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.23 ACT.4: 4 residues within 4Å: Chain A: R.180, K.183, K.187, Y.188 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.187, A:Y.188 Salt bridges: A:R.180, A:K.183 ACT.12: 6 residues within 4Å: Chain B: G.62, T.93, V.95, R.96, E.145, R.149 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.145 Water bridges: B:R.149 Salt bridges: B:R.96, B:R.149 ACT.13: 2 residues within 4Å: Chain B: E.201, K.210 No protein-ligand interaction detected (PLIP) ACT.14: 4 residues within 4Å: Chain B: E.42, K.45, H.46 Ligands: ZN.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.42 Salt bridges: B:K.45, B:H.46 ACT.15: 3 residues within 4Å: Chain A: N.214, D.216 Chain B: D.248 No protein-ligand interaction detected (PLIP) ACT.16: 6 residues within 4Å: Chain B: A.63, R.64, N.72, D.139, S.140 Ligands: ZN.19 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.63 Hydrogen bonds: B:N.72, B:S.140 Water bridges: B:K.144 Salt bridges: B:K.60, B:K.144

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: E.42, H.46, L.241 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:H.46 ZN.6: 2 residues within 4Å: Chain A: H.23 Ligands: ACT.3 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.23, ACT.3, H2O.6 ZN.7: 4 residues within 4Å: Chain A: D.156, W.159, T.160, R.163 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 ZN.17: 5 residues within 4Å: Chain B: E.42, K.45, H.46, L.241 Ligands: ACT.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.16 ZN.18: 2 residues within 4Å: Chain B: D.156, T.160 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.156, H2O.14, H2O.15 ZN.19: 3 residues within 4Å: Chain B: D.139, S.140 Ligands: ACT.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.139, B:D.139, H2O.15

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.252, B:D.216 Water bridges: A:D.248, A:D.248, A:N.252, B:L.215 GOL.9: 2 residues within 4Å: Chain A: E.201, K.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nrholm, A.B. et al., Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold. J.Med.Chem. (2013)

Release Date

2013-11-20

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Glutamate receptor 2

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