SMTL ID : 8gc2.1

Domoate-bound GluK2 kainate receptor in partially-open conformation 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-MAN-MAN-MAN.1: 8 residues within 4Å: Chain A: R.125, L.128, D.129, R.161, N.345, T.347, T.352, W.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161 NAG-NAG-MAN-MAN-MAN.8: 9 residues within 4Å: Chain D: R.125, D.129, R.161, N.345, T.347, N.348, T.352, W.372, P.374 No protein-ligand interaction detected (PLIP)

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.238, E.363, D.393, S.396, N.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.363 NAG-NAG.6: 4 residues within 4Å: Chain C: Y.238, E.363, S.396, N.397 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.238

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

NAG-NAG-MAN-BMA-MAN.3: 3 residues within 4Å: Chain A: E.217, N.242, S.360 No protein-ligand interaction detected (PLIP)

3 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.4: 7 residues within 4Å: Chain B: R.125, D.129, R.161, N.345, N.348, T.352, P.374 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.161, B:R.161 NAG-NAG-BMA-MAN-MAN.5: 5 residues within 4Å: Chain C: R.125, D.129, N.345, T.347, T.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 9 residues within 4Å: Chain C: F.134, E.217, H.220, N.242, K.387, G.738, S.739, P.740, R.742 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.740

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

NAG.9: 2 residues within 4Å: Chain A: N.379, T.381 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: A.389, N.390, D.393 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.389 NAG.12: 4 residues within 4Å: Chain B: N.379, M.380, T.381, Q.384 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.381, B:Q.384 Hydrogen bonds: B:Q.384 NAG.13: 2 residues within 4Å: Chain B: H.220, N.242 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain C: N.379, T.381 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.379 NAG.16: 5 residues within 4Å: Chain C: A.389, N.390, I.391, T.392, D.393 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.391 NAG.18: 3 residues within 4Å: Chain D: V.241, N.242, L.361 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain D: N.379, Q.384 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.384

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

DOQ.11: 15 residues within 4Å: Chain A: E.408, K.454, Y.455, G.456, P.483, L.484, A.485, R.490, V.652, E.653, D.654, G.655, A.656, T.657, E.705 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.455 Hydrogen bonds: A:Y.455, A:G.456, A:P.483, A:A.485, A:D.654, A:A.656, A:T.657, A:E.705 Salt bridges: A:R.490, A:K.729 DOQ.14: 13 residues within 4Å: Chain B: E.407, K.454, Y.455, P.483, L.484, A.485, V.652, E.653, G.655, A.656, T.657, N.688, Y.731 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.455 Hydrogen bonds: B:Y.455, B:A.485, B:A.656, B:T.657, B:Y.731 Salt bridges: B:R.490 DOQ.17: 14 residues within 4Å: Chain C: K.454, Y.455, G.456, A.457, A.485, R.490, V.652, D.654, G.655, A.656, T.657, N.688, E.705, K.729 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.455, C:Y.455, C:Y.455, C:A.457, C:V.652 Hydrogen bonds: C:Y.455, C:G.456, C:G.456, C:A.485, C:D.654, C:D.654, C:A.656, C:T.657, C:E.705, C:K.729, C:K.729 Salt bridges: C:K.454, C:R.490, C:K.729, C:K.729

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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