SMTL ID : 4o3b.1

Crystal structure of an open/closed glua2 ligand-binding domain dimer at 1.91 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.144, R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.144 Salt bridges: A:K.144, A:R.148, A:R.163 SO4.2: 2 residues within 4Å: Chain A: R.172, E.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.176 Salt bridges: A:R.172 SO4.3: 6 residues within 4Å: Chain A: S.217 Chain B: M.107, S.108, D.248 Ligands: GOL.13, GOL.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.108, A:S.217, A:S.217 Water bridges: B:S.108 SO4.11: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:S.140, B:R.148 Salt bridges: B:K.144, B:R.148

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: K.116, K.185, G.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 GOL.5: 6 residues within 4Å: Chain A: P.105, F.106, S.108 Chain B: S.217, K.218, G.219 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.218, A:P.105 Water bridges: B:L.109, B:S.217, B:S.217, B:G.219, A:S.108, A:N.242 GOL.6: 2 residues within 4Å: Chain A: V.99, K.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.99 Water bridges: A:W.71, A:K.226 GOL.12: 3 residues within 4Å: Chain B: K.116, K.185, G.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.185 GOL.13: 8 residues within 4Å: Chain A: S.217, K.218, G.219 Chain B: P.105, M.107, S.108, N.242 Ligands: SO4.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.108, B:N.242, A:S.217, A:K.218 Water bridges: A:L.109 GOL.14: 7 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248, N.252 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.252

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

CL.7: 1 residues within 4Å: Chain A: K.117 Ligand excluded by PLIP

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

PEG.8: 7 residues within 4Å: Chain A: S.108, L.109, S.194, T.195, E.198, N.214, S.217 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.198, A:N.214, A:S.217 Water bridges: B:S.108

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

ACT.9: 4 residues within 4Å: Chain A: Y.61, T.91, R.96, S.142 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.91, A:S.142 Water bridges: A:T.91, A:R.96, A:S.142, A:S.142 Salt bridges: A:R.96

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.10: 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: 10 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:T.91, B:S.142, B:T.143, E.10, E.10, E.10 Water bridges: B:E.193, B:E.193 Salt bridges: B:R.96

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

PG4.15: 5 residues within 4Å: Chain B: K.144, R.148, W.159, R.163, F.170 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.144, B:K.144, B:R.148, B:R.148, B:R.163 Water bridges: B:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krintel, C. et al., L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain. Febs J. (2014)

Release Date

2014-04-16

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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