SMTL ID : 8bn5.1

Crystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1) in complex with GABA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.92, V.95, D.96, R.232 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.92, A:V.95, A:D.96, H2O.2, H2O.6 CA.7: 4 residues within 4Å: Chain B: E.92, V.95, D.96, R.232 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.92, B:V.95, B:D.96, H2O.6, H2O.8 CA.8: 1 residues within 4Å: Chain B: D.233 No protein-ligand interaction detected (PLIP)

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

CL.2: 4 residues within 4Å: Chain A: K.99, R.232 Chain B: K.99, R.232 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.99, R.100 Chain B: I.87, K.99, R.100 Ligand excluded by PLIP

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: L.61, N.63, S.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.65

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.4: 13 residues within 4Å: Chain A: E.11, Y.57, A.84, I.85, T.86, R.91, Y.104, A.137, V.138, W.192, D.193, V.196, Y.221 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.104 Hydrogen bonds: A:A.84, A:T.86, A:T.86, A:D.193 Salt bridges: A:R.91 ABU.10: 12 residues within 4Å: Chain B: E.11, Y.57, A.84, I.85, T.86, R.91, Y.104, A.137, W.192, D.193, V.196, Y.221 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.104 Hydrogen bonds: B:E.11, B:T.86 Salt bridges: B:R.91

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

EDO.5: 9 residues within 4Å: Chain A: Y.104, S.105, V.106, Y.141, S.215, I.216, S.217, S.218, K.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.104, A:V.106, A:S.215, A:S.218, A:K.219 EDO.6: 8 residues within 4Å: Chain A: T.88, P.89, E.90, A.137, E.140, Y.141, K.219 Chain B: D.244 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.137, A:K.219, B:D.244 EDO.11: 9 residues within 4Å: Chain B: Y.104, S.105, V.106, Y.141, N.214, I.216, S.217, S.218, K.219 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.104, B:V.106, B:N.214, B:N.214, B:S.218, B:K.219 Water bridges: B:Y.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piot, L. et al., GluD1 binds GABA and controls inhibitory plasticity. Science (2023)

Release Date

2023-11-22

Peptides

Glutamate receptor ionotropic, delta-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, delta-1

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