SMTL ID : 5elv.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504-N775) in complex with glutamate and BPAM-521 at 1.92 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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 SO4.2: 2 residues within 4Å: Chain A: M.19, R.31 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.31, A:R.31, A:Y.32 Salt bridges: A:R.31 SO4.3: 3 residues within 4Å: Chain A: Y.94, R.149 Chain B: K.240 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.240, A:R.149 Hydrogen bonds: A:Y.94 SO4.14: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 Water bridges: B:K.144, B:K.144, B:R.148, B:R.148 Salt bridges: B:K.144, B:R.148

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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:R.163 GOL.5: 5 residues within 4Å: Chain A: S.108, S.194, T.195, E.198, N.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.108, A:S.194, A:E.198, A:N.214 Water bridges: A:S.108 GOL.15: 5 residues within 4Å: Chain B: S.108, S.194, E.198, K.210, N.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.194, B:E.198, B:K.210, B:K.210, B:N.214 GOL.16: 4 residues within 4Å: Chain B: R.148, W.159, R.163 Ligands: ACT.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.148, B:W.159, B:R.163, B:R.163

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

CL.6: 1 residues within 4Å: Chain A: R.163 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.21, N.22 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP

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

ACT.8: 3 residues within 4Å: Chain A: I.152, A.153 Chain B: K.249 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.249 Hydrophobic interactions: A:I.152 Hydrogen bonds: A:A.153 ACT.9: 2 residues within 4Å: Chain A: Y.256, D.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.257 ACT.10: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.216 ACT.11: 4 residues within 4Å: Chain A: D.38, E.42, L.250, K.253 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.250 Hydrogen bonds: A:E.42 Salt bridges: A:K.253 ACT.18: 1 residues within 4Å: Chain B: K.82 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82 ACT.19: 2 residues within 4Å: Chain B: D.58, N.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.72 Water bridges: B:G.73 ACT.20: 5 residues within 4Å: Chain B: K.144, R.148, R.163, F.170 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.170 Salt bridges: B:K.144, B:R.148 ACT.21: 7 residues within 4Å: Chain B: I.113, S.123, A.124, E.125, G.212, G.213, L.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.124, B:E.125, B:G.213, B:G.213 ACT.22: 5 residues within 4Å: Chain A: Y.94 Chain B: H.46, L.236, A.237, K.240 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.46, B:K.240

2 x 5PX: 4-Cyclopropyl-3,4-dihydro-7-hydroxy-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

5PX.12: 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: 5PX.25 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.247, A:P.105 Hydrogen bonds: A:S.108, A:G.219 5PX.25: 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: 5PX.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.105, A:L.247 Hydrogen bonds: B:S.108, B:G.219

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.13: 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.13, E.13 Water bridges: A:E.193, A:E.193 Salt bridges: A:R.96 GLU.26: 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.26, E.26 Water bridges: B:K.144, B:E.193, B:E.193 Salt bridges: B:R.96

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

PEG.23: 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 PEG.24: 4 residues within 4Å: Chain B: M.19, H.23, E.24, R.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krintel, C. et al., Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2. Biophys.J. (2016)

Release Date

2016-05-04

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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