SMTL ID : 8bn2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

7 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

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.3 CA.2: 2 residues within 4Å: Chain A: D.233 Chain B: D.233 No protein-ligand interaction detected (PLIP) CA.3: 1 residues within 4Å: Chain A: G.113 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.113 CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 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.10 CA.11: 1 residues within 4Å: Chain B: G.113 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.113, H2O.6, H2O.10 CA.12: 4 residues within 4Å: Chain B: A.84, Y.104, D.193, Y.221 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain A: K.99, R.232 Chain B: K.99, R.232 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: K.99 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.6: 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

1 x DSN: D-SERINE(Non-covalent)

DSN.7: 12 residues within 4Å: Chain A: Y.57, A.84, I.85, T.86, R.91, Y.104, S.136, A.137, V.138, W.192, D.193, Y.221 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.84, A:T.86, A:D.193, A:D.193 Water bridges: A:A.137 Salt bridges: A:R.91

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

EDO.8: 5 residues within 4Å: Chain A: T.64, S.65, W.66, I.74, V.94 No protein-ligand interaction detected (PLIP) EDO.9: 9 residues within 4Å: Chain A: Y.104, S.105, V.106, Y.141, S.215, I.216, S.217, S.218, K.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.106, A:S.215, A:S.218, A:S.218, A:K.219 Water bridges: A: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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