SMTL ID : 4u4s.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and BPAM25 at 1.90 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 3C1: 4-ethyl-3,4-dihydro-2H-pyrido[4,3-e][1,2,4]thiadiazine 1,1-dioxide(Non-covalent)

3C1.1: 15 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: 3C1.12, ACT.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.219 3C1.12: 14 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242 Chain B: P.105, S.108, S.217, K.218, G.219 Ligands: 3C1.1, ACT.7 No protein-ligand interaction detected (PLIP)

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

SO4.2: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Water bridges: A:R.148, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.3: 3 residues within 4Å: Chain A: Y.94, R.149 Chain B: K.240 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.149, B:K.240 SO4.13: 6 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 Ligands: ACT.18 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 Water bridges: B:K.144, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: C.47, S.229, L.230, A.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.229 Water bridges: A:A.233 GOL.5: 3 residues within 4Å: Chain A: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:W.159 GOL.14: 6 residues within 4Å: Chain B: G.62, A.63, R.64, W.71, R.96, E.145 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.64, B:R.64, B:R.96, B:R.96 Water bridges: B:G.141, B:E.145, B:R.148, B:R.148 GOL.15: 4 residues within 4Å: Chain B: R.148, W.159, R.163 Ligands: ACT.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.148, B:R.163

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

ACT.6: 3 residues within 4Å: Chain A: H.46, A.237 Chain B: Y.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.46 Salt bridges: A:H.46 ACT.7: 5 residues within 4Å: Chain A: M.107, S.108, D.248 Chain B: S.217 Ligands: 3C1.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.217, B:S.217, A:S.108 ACT.8: 1 residues within 4Å: Chain A: R.31 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.31 Salt bridges: A:R.31 ACT.9: 5 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104, N.235 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.104 Hydrogen bonds: A:E.97, A:D.101, A:F.102 ACT.17: 3 residues within 4Å: Chain B: M.19, H.23, R.31 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.31 ACT.18: 6 residues within 4Å: Chain B: K.144, R.148, R.163, F.170 Ligands: SO4.13, GOL.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.163 Water bridges: B:S.168 Salt bridges: B:K.144, B:R.148 ACT.19: 5 residues within 4Å: Chain A: S.217 Chain B: M.107, S.108, D.248 Ligands: 3C1.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.248, A:S.217 Water bridges: B:D.248 ACT.20: 5 residues within 4Å: Chain A: K.104, N.235 Chain B: E.97, D.101, F.102 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.97, B:D.101, B:F.102 Salt bridges: A:K.104

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

CL.10: 1 residues within 4Å: Chain A: A.153 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.11: 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.11, E.11 Water bridges: A:E.193, A:E.193 Salt bridges: A:R.96 GLU.22: 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 13 PLIP interactions: 11 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.22, E.22 Water bridges: B:E.193, B:E.193 Salt bridges: B:R.96

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

PEG.16: 4 residues within 4Å: Chain B: E.27, G.28, R.31, K.52 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.28, B:R.31, B:R.31, B:K.52 Water bridges: B:Y.32, B:Y.32

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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