SMTL ID : 9b39.1

Kainate receptor GluK2 in complex with agonist glutamate with asymmetric ligand-binding domain layer

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: H.225, Y.251, H.253, N.275, R.775 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.775, A:R.775 NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: R.158, D.162, R.194, N.378, N.381, T.385, P.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:Q.165, A:P.407, A:R.158, A:R.158 NAG-NAG-BMA-MAN-MAN.6: 7 residues within 4Å: Chain C: E.250, Y.251, H.253, N.275, G.771, S.772, P.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain C: R.158, D.162, R.194, N.378, T.380, N.381, T.385 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.158, C:R.158 NAG-NAG-BMA-MAN-MAN.8: 4 residues within 4Å: Chain C: Y.271, E.396, S.429, N.430 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.271, C:Y.271

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.412, T.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain D: R.158, N.378, T.380, T.385 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.158, D:R.158 NAG-NAG-BMA.10: 2 residues within 4Å: Chain D: N.412, T.414 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.4: 2 residues within 4Å: Chain A: Y.271, N.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.271 NAG-NAG.5: 7 residues within 4Å: Chain B: H.253, G.273, N.275, S.393, L.394, K.395, K.418 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.395, B:K.395, B:K.395, B:K.418

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.11: 10 residues within 4Å: Chain A: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, M.737, E.738, Y.764 11 PLIP interactions: 7 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.488, A:Y.488, A:P.516 Hydrogen bonds: A:A.518, A:A.689, A:Y.764, E.11, E.11, E.11, E.11 Salt bridges: A:R.523 GLU.16: 8 residues within 4Å: Chain B: Y.488, P.516, L.517, A.518, R.523, I.538, N.721, E.738 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:Y.488 Hydrogen bonds: B:P.516, B:A.518, B:N.721, B:E.738, B:E.738 Salt bridges: B:R.523 GLU.22: 9 residues within 4Å: Chain C: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, E.738 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:Y.488 Hydrogen bonds: C:P.516, C:A.518, C:A.689, C:T.690 Salt bridges: C:R.523 GLU.29: 10 residues within 4Å: Chain D: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, E.738, Y.764 10 PLIP interactions: 3 Ligand-Ligand interactions, 7 interactions with chain D Hydrogen bonds: E.29, E.29, E.29, D:P.516, D:A.518, D:A.689, D:T.690, D:E.738 Hydrophobic interactions: D:Y.488 Salt bridges: D:R.523

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

NAG.12: 2 residues within 4Å: Chain A: N.67, T.69 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: P.72, N.73 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.423, I.424, T.425 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: R.543, C.750, N.751 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.67, T.69 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: P.72, N.73 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.378, T.380, N.381, T.385 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.412 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain B: R.543, P.545, N.546, L.729, T.730, S.731, D.732 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.67, T.69 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.73 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.412, T.414 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.423, T.425 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: R.543, N.546 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: R.748, N.749, N.751 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.67, R.68 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.73 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: S.429, N.430 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: K.544, N.546 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: P.545, L.729, N.751 Ligands: NAG.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Kainate receptor channel opening and gating mechanism. Nature (2024)

Release Date

2024-05-22

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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