SMTL ID : 8blj.1 (2 other biounits)

Crystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1), apo state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.92, S.93, V.95, D.96, H.227 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.92, A:E.92, A:D.96, H2O.1, H2O.4 CA.2: 3 residues within 4Å: Chain A: A.84, D.193, Y.221 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.193 CA.3: 1 residues within 4Å: Chain A: P.149 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: E.92, V.95, D.96 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.92, B:E.92, B:V.95, B:D.96, H2O.4 CA.8: 4 residues within 4Å: Chain B: M.102, V.194, A.195, E.198 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.198

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

CL.4: 4 residues within 4Å: Chain A: K.99, R.232 Chain B: K.99, R.232 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain A: R.100, S.217, S.218, K.219 Chain B: R.100, D.103, Q.243 Ligand excluded by PLIP

2 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63, A:S.65 NAG.9: 3 residues within 4Å: Chain B: L.61, N.63, S.65 No protein-ligand interaction detected (PLIP)

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,Isoform 2 of Glutamate receptor ionotropic, delta-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1

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