SMTL ID : 5kc8.1

Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

CA.1: 2 residues within 4Å: Chain A: E.61, E.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:E.64, A:E.64, H2O.1, H2O.7 CA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain B: E.61, E.64 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.61, B:E.64, B:E.64, H2O.10, H2O.16 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.3: 5 residues within 4Å: Chain A: I.336 Chain B: C.63, N.67, S.334, C.335 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.335 EDO.4: 2 residues within 4Å: Chain A: Q.60 Chain B: A.91 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:A.91, A:Q.60 Hydrogen bonds: A:N.54 EDO.5: 8 residues within 4Å: Chain A: Q.100, R.101, S.102, R.127, E.244, E.301, I.302, S.303 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.102, A:S.102, A:R.127, A:R.127, A:I.302, A:S.303, A:S.303 Water bridges: A:S.102, A:S.102 EDO.8: 5 residues within 4Å: Chain A: C.63, N.67, S.334, C.335 Chain B: I.336 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.335 EDO.9: 2 residues within 4Å: Chain A: A.91 Chain B: Q.60 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:A.91, B:Q.60 Hydrogen bonds: B:N.54 EDO.10: 8 residues within 4Å: Chain B: Q.100, R.101, S.102, R.127, E.244, E.301, I.302, S.303 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.102, B:S.102, B:R.127, B:R.127, B:I.302, B:S.303, B:S.303 Water bridges: B:S.102, B:S.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elegheert, J. et al., Structural basis for integration of GluD receptors within synaptic organizer complexes. Science (2016)

Release Date

2016-07-27

Peptides

Glutamate receptor ionotropic, delta-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor ionotropic, delta-2