SMTL ID : 9b38.1

Kainate receptor GluK2 in complex with agonist glutamate with pseudo 4-fold symmetrical ligand-binding domain layer

Coordinates

PDB Format Compare

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: H.225, E.250, Y.251, H.253, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 2 residues within 4Å: Chain A: Y.271, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 5 residues within 4Å: Chain B: R.158, D.162, N.378, T.380, N.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 5 residues within 4Å: Chain C: H.225, E.250, Y.251, H.253, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 2 residues within 4Å: Chain C: Y.271, N.430 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain D: R.158, N.378, T.380, N.381 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.154

6 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.2: 5 residues within 4Å: Chain A: R.158, N.378, T.385 Ligands: MAN.18, MAN.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158 NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain B: N.412, Q.417 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain C: R.158, N.378, T.385 Ligands: MAN.31, MAN.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.158, C:R.158 NAG-NAG-BMA.10: 1 residues within 4Å: Chain C: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 2 residues within 4Å: Chain D: N.412, Q.417 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.5: 4 residues within 4Å: Chain B: E.250, H.253, N.275, K.395 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: E.250, H.253, N.275, K.395 No protein-ligand interaction detected (PLIP)

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.15: 13 residues within 4Å: Chain A: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, N.721, L.736, M.737, E.738, Y.764 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.488, A:E.738 Hydrogen bonds: A:A.518, A:A.689, A:T.690, A:T.690, A:M.737, A:Y.764, A:Y.764, E.15, E.15 Salt bridges: A:R.523 GLU.23: 12 residues within 4Å: Chain B: Y.488, P.516, A.518, R.523, V.685, G.688, A.689, T.690, N.721, M.737, E.738, Y.764 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:Y.488 Hydrogen bonds: B:A.518, B:A.689, B:E.738, B:E.738 Salt bridges: B:R.523 GLU.28: 13 residues within 4Å: Chain C: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, N.721, L.736, M.737, E.738, Y.764 12 PLIP interactions: 10 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Y.488, C:E.738 Hydrogen bonds: C:A.518, C:A.689, C:T.690, C:T.690, C:M.737, C:Y.764, C:Y.764, E.28, E.28 Salt bridges: C:R.523 GLU.36: 12 residues within 4Å: Chain D: Y.488, P.516, A.518, R.523, V.685, G.688, A.689, T.690, N.721, M.737, E.738, Y.764 6 PLIP interactions: 6 interactions with chain D, Hydrophobic interactions: D:Y.488 Hydrogen bonds: D:A.518, D:A.689, D:E.738, D:E.738 Salt bridges: D:R.523

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

NAG.16: 3 residues within 4Å: Chain A: N.67, T.69, W.368 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: P.72, N.73 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.423 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: R.543, N.546 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: R.543, N.749, N.751 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.67, T.69 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: P.72, N.73 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: R.543, N.546, N.751 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: L.729, N.751 Ligands: NAG.26 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.67, T.69, W.368 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: P.72, N.73 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.423 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: R.543, N.546 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: R.543, N.749, N.751 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.67, T.69 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: P.72, N.73 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain D: R.543, N.546, N.751 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: L.729, N.751 Ligands: NAG.39 Ligand excluded by PLIP

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

MAN.18: 4 residues within 4Å: Chain A: R.158, D.162, P.407 Ligands: NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:P.407 MAN.19: 2 residues within 4Å: Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) MAN.31: 4 residues within 4Å: Chain C: R.158, D.162, P.407 Ligands: NAG-NAG-BMA.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.162, C:P.407 MAN.32: 2 residues within 4Å: Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9 No protein-ligand interaction detected (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

Glutamate receptor ionotropic, kainate 2

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