SMTL ID : 5jei.1

Crystal structure of the GluA2 LBD in complex with FW

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-tetramer

Ligands

4 x FWD: 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID(Non-covalent)

FWD.1: 15 residues within 4Å: Chain A: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:P.89, A:T.91, A:T.91, A:S.142, A:S.142, A:T.143, A:T.143, A:E.193 Water bridges: A:E.193 Salt bridges: A:R.96 FWD.15: 15 residues within 4Å: Chain B: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:P.89, B:T.91, B:T.91, B:S.142, B:S.142, B:T.143, B:T.143, B:E.193 Water bridges: B:E.193 Salt bridges: B:R.96 FWD.29: 15 residues within 4Å: Chain C: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:P.89, C:T.91, C:T.91, C:S.142, C:S.142, C:T.143, C:T.143, C:E.193 Water bridges: C:E.193 Salt bridges: C:R.96 FWD.43: 15 residues within 4Å: Chain D: E.13, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:P.89, D:T.91, D:T.91, D:S.142, D:S.142, D:T.143, D:T.143, D:E.193 Water bridges: D:E.193 Salt bridges: D:R.96

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: R.148, W.159, R.163 Chain D: K.20, E.30 Ligands: PG4.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:W.159 Salt bridges: A:R.163, D:K.20 Water bridges: D:K.20, D:K.20 PO4.3: 4 residues within 4Å: Chain A: M.19, H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.24, A:E.24 Water bridges: A:E.24, A:R.31, A:Y.32 Salt bridges: A:H.23, A:R.31 PO4.16: 4 residues within 4Å: Chain B: R.148, W.159, R.163 Ligands: PG4.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.159 Salt bridges: B:R.163 PO4.17: 4 residues within 4Å: Chain B: M.19, H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.24, B:E.24 Water bridges: B:E.24, B:R.31, B:Y.32 Salt bridges: B:H.23, B:R.31 PO4.30: 6 residues within 4Å: Chain B: K.20, E.30 Chain C: R.148, W.159, R.163 Ligands: PG4.35 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Water bridges: B:K.20, B:K.20 Salt bridges: B:K.20, C:R.163 Hydrogen bonds: C:W.159 PO4.31: 4 residues within 4Å: Chain C: M.19, H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.24, C:E.24 Water bridges: C:E.24, C:R.31, C:Y.32 Salt bridges: C:H.23, C:R.31 PO4.44: 4 residues within 4Å: Chain D: R.148, W.159, R.163 Ligands: PG4.49 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.159 Salt bridges: D:R.163 PO4.45: 4 residues within 4Å: Chain D: M.19, H.23, E.24, R.31 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.24, D:E.24 Water bridges: D:E.24, D:R.31, D:Y.32 Salt bridges: D:H.23, D:R.31

8 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 8 residues within 4Å: Chain A: E.198, E.201, Q.202, M.209, K.210, V.211, G.212 Ligands: ETE.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.210, A:K.210 PG4.7: 7 residues within 4Å: Chain A: K.144, R.148, W.159, R.163, F.170 Chain D: E.30 Ligands: PO4.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.144 Water bridges: A:R.148, D:K.20 PG4.18: 8 residues within 4Å: Chain B: E.198, E.201, Q.202, M.209, K.210, V.211, G.212 Ligands: ETE.24 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.210, B:K.210 PG4.21: 6 residues within 4Å: Chain B: K.144, R.148, W.159, R.163, F.170 Ligands: PO4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.144 Water bridges: B:R.148 PG4.32: 8 residues within 4Å: Chain C: E.198, E.201, Q.202, M.209, K.210, V.211, G.212 Ligands: ETE.38 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.210, C:K.210 PG4.35: 7 residues within 4Å: Chain B: E.30 Chain C: K.144, R.148, W.159, R.163, F.170 Ligands: PO4.30 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.144 Water bridges: C:R.148, B:K.20 PG4.46: 8 residues within 4Å: Chain D: E.198, E.201, Q.202, M.209, K.210, V.211, G.212 Ligands: ETE.52 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.210, D:K.210 PG4.49: 6 residues within 4Å: Chain D: K.144, R.148, W.159, R.163, F.170 Ligands: PO4.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.144 Water bridges: D:R.148

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

PEG.5: 6 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 Ligands: TOE.20 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.217, A:S.217 Water bridges: A:N.214, A:N.214, A:N.214, A:S.217 PEG.11: 5 residues within 4Å: Chain A: M.18, E.33, R.203, W.254, K.258 No protein-ligand interaction detected (PLIP) PEG.13: 7 residues within 4Å: Chain A: Q.130, T.131, E.132, I.133, A.134, Y.135, Y.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.130 Water bridges: A:Y.161 PEG.19: 6 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 Ligands: TOE.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.217, B:S.217 Water bridges: B:N.214, B:N.214, B:N.214, B:S.217 PEG.25: 8 residues within 4Å: Chain B: M.18, E.33, R.203, W.254, K.258 Chain C: T.160, Y.161, S.164 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.160 Water bridges: C:S.164 PEG.27: 7 residues within 4Å: Chain B: Q.130, T.131, E.132, I.133, A.134, Y.135, Y.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.130 Water bridges: B:Y.161 PEG.33: 6 residues within 4Å: Chain C: N.214, L.215, D.216, S.217 Chain D: D.248 Ligands: TOE.48 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.217, C:S.217 Water bridges: C:N.214, C:N.214, C:N.214, C:S.217 PEG.39: 5 residues within 4Å: Chain C: M.18, E.33, R.203, W.254, K.258 No protein-ligand interaction detected (PLIP) PEG.41: 7 residues within 4Å: Chain C: Q.130, T.131, E.132, I.133, A.134, Y.135, Y.161 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.130 Water bridges: C:Y.161 PEG.47: 6 residues within 4Å: Chain C: D.248 Chain D: N.214, L.215, D.216, S.217 Ligands: TOE.34 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.217, D:S.217 Water bridges: D:N.214, D:N.214, D:N.214, D:S.217 PEG.53: 8 residues within 4Å: Chain A: T.160, Y.161, S.164 Chain D: M.18, E.33, R.203, W.254, K.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.160 Water bridges: A:S.164 PEG.55: 7 residues within 4Å: Chain D: Q.130, T.131, E.132, I.133, A.134, Y.135, Y.161 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.130 Water bridges: D:Y.161

4 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.6: 13 residues within 4Å: Chain A: P.105, F.106, M.107, S.108, N.242, L.247, D.248, K.251 Chain B: P.105, S.217, K.218, G.219 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.108, A:S.108 TOE.20: 13 residues within 4Å: Chain A: P.105, S.217, K.218, G.219 Chain B: P.105, F.106, M.107, S.108, N.242, L.247, D.248, K.251 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.108, B:S.108 TOE.34: 13 residues within 4Å: Chain C: P.105, F.106, M.107, S.108, N.242, L.247, D.248, K.251 Chain D: P.105, S.217, K.218, G.219 Ligands: PEG.47 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.108, C:S.108 TOE.48: 13 residues within 4Å: Chain C: P.105, S.217, K.218, G.219 Chain D: P.105, F.106, M.107, S.108, N.242, L.247, D.248, K.251 Ligands: PEG.33 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.108, D:S.108

4 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.8: 6 residues within 4Å: Chain A: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.4, A:D.84 PG0.22: 6 residues within 4Å: Chain B: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.4, B:D.84 PG0.36: 6 residues within 4Å: Chain C: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.4, C:D.84 PG0.50: 6 residues within 4Å: Chain D: K.4, V.7, G.81, K.82, A.83, D.84 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.4, D:D.84

8 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.9: 8 residues within 4Å: Chain A: K.4, V.6, C.47, F.49, D.84, S.228, S.229, L.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.229, A:S.229 Water bridges: A:S.229 ETE.10: 11 residues within 4Å: Chain A: K.117, E.201, Q.202, T.208, M.209, Y.256, C.261, G.262, S.263, G.264 Ligands: PG4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117, A:Q.202 ETE.23: 8 residues within 4Å: Chain B: K.4, V.6, C.47, F.49, D.84, S.228, S.229, L.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.229, B:S.229 Water bridges: B:S.229 ETE.24: 11 residues within 4Å: Chain B: K.117, E.201, Q.202, T.208, M.209, Y.256, C.261, G.262, S.263, G.264 Ligands: PG4.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.117, B:Q.202 ETE.37: 8 residues within 4Å: Chain C: K.4, V.6, C.47, F.49, D.84, S.228, S.229, L.230 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.229, C:S.229 Water bridges: C:S.229 ETE.38: 11 residues within 4Å: Chain C: K.117, E.201, Q.202, T.208, M.209, Y.256, C.261, G.262, S.263, G.264 Ligands: PG4.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.117, C:Q.202 ETE.51: 8 residues within 4Å: Chain D: K.4, V.6, C.47, F.49, D.84, S.228, S.229, L.230 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.229, D:S.229 Water bridges: D:S.229 ETE.52: 11 residues within 4Å: Chain D: K.117, E.201, Q.202, T.208, M.209, Y.256, C.261, G.262, S.263, G.264 Ligands: PG4.46 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.117, D:Q.202

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

EDO.12: 7 residues within 4Å: Chain A: L.12, E.13, S.14, T.174, A.175, V.178, I.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.14, A:S.14 Water bridges: A:S.14 EDO.26: 7 residues within 4Å: Chain B: L.12, E.13, S.14, T.174, A.175, V.178, I.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.14, B:S.14 Water bridges: B:S.14 EDO.40: 7 residues within 4Å: Chain C: L.12, E.13, S.14, T.174, A.175, V.178, I.200 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.14, C:S.14 Water bridges: C:S.14 EDO.54: 7 residues within 4Å: Chain D: L.12, E.13, S.14, T.174, A.175, V.178, I.200 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.14, D:S.14 Water bridges: D:S.14

4 x NA: SODIUM ION(Non-functional Binders)

NA.14: 1 residues within 4Å: Chain A: E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.198 Water bridges: A:K.251, A:K.251 NA.28: 1 residues within 4Å: Chain B: E.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.198 Water bridges: B:K.251, B:K.251 NA.42: 1 residues within 4Å: Chain C: E.198 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.198 Water bridges: C:K.251, C:K.251 NA.56: 1 residues within 4Å: Chain D: E.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.198 Water bridges: D:K.251, D:K.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salazar, H. et al., Mechanism of partial agonism in AMPA-type glutamate receptors. Nat Commun (2017)

Release Date

2017-02-22

Peptides

Glutamate receptor 2,Glutamate receptor 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glutamate receptor 2,Glutamate receptor 2