SMTL ID : 4u4x.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and BPAM37 at 1.56 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

2 x 3C2: 4-ethyl-3,4-dihydro-2H-pyrido[3,2-e][1,2,4]thiadiazine 1,1-dioxide(Non-covalent)

3C2.1: 14 residues within 4Å: Chain A: I.92, P.105, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Ligands: 3C2.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.219 3C2.11: 14 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Chain B: I.92, P.105, S.108, S.217, K.218, G.219 Ligands: 3C2.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.219

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

SO4.2: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: GOL.8 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.139, A:S.140, A:S.140 Water bridges: A:K.144, A:K.144, A:R.148, A:R.148 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 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:N.235 Salt bridges: B:K.104 Hydrogen bonds: A:D.101, A:D.101, A:F.102 SO4.12: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 Salt bridges: B:K.144, B:R.148 SO4.13: 1 residues within 4Å: Chain B: R.31 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.31, B:Y.32 Salt bridges: B:R.31 SO4.14: 5 residues within 4Å: Chain A: K.104, N.235 Chain B: E.97, D.101, F.102 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.101, B:D.101, B:F.102 Water bridges: A:N.235, A:N.235, A:N.235 Salt bridges: A:K.104

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 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: 12 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, A:E.193, E.4, E.4 Water bridges: A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.15: 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:S.142, B:T.143, B:T.143, B:E.193, E.15, E.15 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

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

ACT.5: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.217, A:D.248 ACT.16: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.214 Water bridges: A:S.217 ACT.17: 3 residues within 4Å: Chain B: R.148, W.159, R.163 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.148 Water bridges: B:R.148, B:W.159 Salt bridges: B:R.148, B:R.163 ACT.18: 3 residues within 4Å: Chain A: Y.94 Chain B: H.46, A.237 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.46 Hydrophobic interactions: A:Y.94

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.148, W.159, R.163 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:W.159, A:R.163, A:R.163 GOL.7: 3 residues within 4Å: Chain A: N.3, K.4, T.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.3, A:T.5 GOL.8: 7 residues within 4Å: Chain A: D.139, K.144, R.148, R.163, F.170 Ligands: SO4.2, GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.144, A:R.148, A:R.163 Water bridges: A:D.139, A:S.168

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

PEG.9: 4 residues within 4Å: Chain A: E.27, G.28, R.31, K.52 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.28, A:R.31, A:K.52 Water bridges: A:R.31, A:Y.32, A:Y.32 PEG.10: 3 residues within 4Å: Chain A: K.116, P.205, D.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116, A:D.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francotte, P. et al., Positive Allosteric Modulators of 2-Amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic Acid Receptors Belonging to 4-Cyclopropyl-3,4-dihydro-2H-1,2,4-pyridothiadiazine Dioxides and Diversely Chloro-Substituted 4-Cyclopropyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides. J.Med.Chem. (2014)

Release Date

2014-11-19

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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