SMTL ID : 5buu.1

Crystal structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM-321 at 2.07 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x 4V6: (3R)-7-chloro-2,3,4-trimethyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

4V6.1: 14 residues within 4Å: Chain A: I.92, P.105, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, S.108, V.238, L.239, S.242 Ligands: SO4.5, 4V6.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.105, B:V.238, B:L.239 Hydrogen bonds: A:G.219 Halogen bonds: A:S.108 4V6.6: 14 residues within 4Å: Chain A: K.104, P.105, S.108, V.238, L.239, S.242 Chain B: I.92, P.105, S.108, S.217, K.218, G.219 Ligands: 4V6.1, SO4.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.238, A:L.239, B:P.105 Hydrogen bonds: B:G.219 Halogen bonds: B:S.108

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 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:T.143, A:T.143, E.2, E.2, E.2 Water bridges: A:G.141, A:E.193 Salt bridges: A:R.96 GLU.7: 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: 11 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:S.142, B:T.143, B:T.143, B:E.193, E.7, E.7, E.7 Water bridges: B:K.144, B:E.193 Salt bridges: B:R.96

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

SO4.3: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.139, A:S.140 Water bridges: A:S.140 Salt bridges: A:K.144, A:R.148 SO4.4: 8 residues within 4Å: Chain A: K.104, P.105, L.239 Chain B: I.92, P.105, K.218, G.219 Ligands: 4V6.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.219 SO4.5: 6 residues within 4Å: Chain A: I.92, K.218, G.219 Chain B: K.104, P.105 Ligands: 4V6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.219 SO4.8: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.139, B:S.140, B:S.140 Water bridges: B:G.141 Salt bridges: B:K.144, B:R.148 SO4.9: 2 residues within 4Å: Chain B: M.19, R.31 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.31, B:R.31 Salt bridges: B:R.31

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 5 residues within 4Å: Chain A: Y.94 Chain B: H.46, A.233, L.236, A.237 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.46, B:A.233, A:Y.94, A:Y.94 EDO.11: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.215 Water bridges: A:S.217, B:D.248 EDO.12: 4 residues within 4Å: Chain A: K.104 Chain B: E.97, D.101, F.102 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.104, B:E.97, B:F.102 EDO.13: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.216 EDO.14: 3 residues within 4Å: Chain B: R.148, W.159, R.163 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsen, A.P. et al., Synthesis and Pharmacology of Mono-, Di-, and Trialkyl-Substituted 7-Chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides Combined with X-ray Structure Analysis to Understand the Unexpected Structure-Activity Relationship at AMPA Receptors. Acs Chem Neurosci (2016)

Release Date

2016-02-17

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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