SMTL ID : 8gc5.1

Domoate-bound GluK2 kainate receptors in non-active conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

5 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.125, N.345, T.347, N.348, T.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain A: E.217, Y.218, H.220, N.242, R.742 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 4 residues within 4Å: Chain B: R.125, D.129, N.345, T.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain C: R.125, D.129, N.345, T.347 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain D: R.125, D.129, R.161, N.345, T.347, N.348, T.352, P.374 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.161

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: 4 residues within 4Å: Chain A: Y.238, E.363, S.396, N.397 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: D.393, S.394, S.396, N.397, R.398 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.7: 5 residues within 4Å: Chain C: E.217, Y.218, H.220, N.242 Ligands: MAN.15 No protein-ligand interaction detected (PLIP)

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

NAG.9: 2 residues within 4Å: Chain A: N.379, T.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.11: 3 residues within 4Å: Chain B: N.379, T.381, Q.384 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.379, B:Q.384, B:Q.384 NAG.12: 2 residues within 4Å: Chain B: H.220, N.242 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain C: N.379, T.381 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.379 NAG.17: 2 residues within 4Å: Chain D: N.379, Q.384 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.379 NAG.18: 3 residues within 4Å: Chain D: E.217, H.220, N.242 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.220

4 x DOQ: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID(Non-covalent)

DOQ.10: 15 residues within 4Å: Chain A: K.454, Y.455, G.456, A.457, P.483, L.484, A.485, R.490, V.652, E.653, D.654, G.655, A.656, T.657, E.705 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.455, A:Y.455, A:A.457, A:D.654 Hydrogen bonds: A:Y.455, A:A.485, A:R.490, A:A.656, A:T.657 Salt bridges: A:R.490 DOQ.13: 13 residues within 4Å: Chain B: E.407, G.453, K.454, Y.455, L.484, A.485, V.652, E.653, D.654, A.656, K.686, N.688, E.705 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.455, B:V.652, B:V.652 Hydrogen bonds: B:E.407, B:Y.455, B:A.485, B:D.654, B:N.688, B:Y.731 DOQ.16: 16 residues within 4Å: Chain C: G.453, K.454, Y.455, P.483, L.484, A.485, R.490, V.652, D.654, G.655, A.656, T.657, K.686, N.688, E.705, Y.731 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.455, C:V.652 Hydrogen bonds: C:Y.455, C:A.485, C:A.656, C:T.657, C:Y.731 Salt bridges: C:R.490 DOQ.19: 14 residues within 4Å: Chain D: K.454, Y.455, P.483, L.484, A.485, R.490, V.652, E.653, D.654, G.655, A.656, T.657, N.688, E.705 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:K.454, D:V.652 Hydrogen bonds: D:A.485, D:A.656, D:T.657, D:E.705, D:E.705 Salt bridges: D:K.454, D:R.490, D:K.729

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.15: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bogdanovic, N. et al., Structural basis for kainate receptor activation by a partial agonist. To Be Published

Release Date

2024-03-13

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

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