SMTL ID : 4o3c.1

Crystal structure of the GLUA2 ligand-binding domain in complex with L-aspartate at 1.50 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 10 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 10 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, A:E.193, D.1, D.1, D.1, D.1 Water bridges: A:E.193 Salt bridges: A:R.96 ASP.10: 10 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, G.141, S.142, T.143, E.193, Y.220 14 PLIP interactions: 10 interactions with chain B, 4 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, B:E.193, D.10, D.10, D.10, D.10 Water bridges: B:E.193 Salt bridges: B:R.96

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

CL.2: 3 residues within 4Å: Chain A: M.107, S.108 Ligands: ACT.4 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: M.107, S.108 Ligands: ACT.13 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: R.31 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31 GOL.12: 2 residues within 4Å: Chain B: R.31 Ligands: SO4.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.31

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

ACT.4: 9 residues within 4Å: Chain A: P.105, F.106, M.107, S.108, N.242 Chain B: S.217, K.218 Ligands: CL.2, LI.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.105, A:S.108, A:S.108 ACT.13: 9 residues within 4Å: Chain A: S.217, K.218 Chain B: P.105, F.106, M.107, S.108, N.242 Ligands: CL.11, LI.14 3 PLIP interactions: 3 interactions with chain B Water bridges: B:P.105, B:S.108, B:S.108

2 x LI: LITHIUM ION(Non-covalent)

LI.5: 4 residues within 4Å: Chain A: N.242, D.248 Chain B: S.217 Ligands: ACT.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.217, H2O.1, H2O.5 LI.14: 4 residues within 4Å: Chain A: S.217 Chain B: N.242, D.248 Ligands: ACT.13 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.217, H2O.11, H2O.15

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

SO4.6: 4 residues within 4Å: Chain A: H.23, E.24, R.31 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:E.24 Salt bridges: A:H.23, A:R.31 SO4.7: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 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 Salt bridges: A:K.144, A:R.148 SO4.8: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.29, A:E.30 Water bridges: A:N.29, A:N.29 SO4.9: 3 residues within 4Å: Chain A: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.159 Salt bridges: A:R.163 SO4.15: 4 residues within 4Å: Chain B: H.23, E.24, R.31 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:E.24 Salt bridges: B:H.23, B:R.31 SO4.16: 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:D.139, 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 SO4.17: 4 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.29, B:E.30 Water bridges: B:N.29, B:N.29 SO4.18: 3 residues within 4Å: Chain B: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.159 Salt 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
A

Glutamate receptor 2

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