SMTL ID : 8f0o.1

cryo-EM structure of homomeric kainate receptor GluK2 in resting (apo) state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

6 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: R.158, N.378, K.379, N.381, T.385 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 2 residues within 4Å: Chain A: H.253, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 6 residues within 4Å: Chain B: R.158, D.162, N.378, T.380, T.385, P.407 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 6 residues within 4Å: Chain C: R.158, D.162, N.378, T.380, N.381, T.385 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.158 NAG-NAG-BMA-MAN-MAN.7: 6 residues within 4Å: Chain C: F.167, E.250, H.253, N.275, Q.417, P.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain D: R.158, D.162, R.194, N.378, T.380, N.381, T.385, P.407 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.194, D:R.194

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: Y.271, D.426, S.427, S.429, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: Y.271, S.429, N.430 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.412, M.413, T.414 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.414 NAG.10: 3 residues within 4Å: Chain B: S.409, N.412, Q.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.409, B:S.409 NAG.11: 1 residues within 4Å: Chain C: N.412 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain D: N.412, Q.417 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bogdanovic, N. et al., Partial agonism in kainate receptors. To Be Published

Release Date

2023-11-08

Peptides

Glutamate receptor ionotropic, kainate 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, kainate 2