SMTL ID : 9b36.1

Open state of kainate receptor GluK2 in complex with agonist glutamate and positive allosteric modulator BPAM344 bound to two concanavalin A dimers. Composite map.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-NAG-GAL-MAN.1: 10 residues within 4Å: Chain A: R.543, K.544, P.545, N.546 Chain H: Y.12, D.16, L.99, Y.100, R.228 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.16 NAG-NAG-BMA-MAN-NAG-GAL-MAN.15: 9 residues within 4Å: Chain C: R.543, P.545, N.546 Chain F: Y.12, L.99, Y.100, S.204, R.228 Ligands: NAG-NAG.16 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.12, F:Y.100, F:R.228, F:R.228

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

NAG-NAG.2: 3 residues within 4Å: Chain A: C.750, N.751 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.67, T.69, L.70, Q.288 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.70 NAG-NAG.6: 3 residues within 4Å: Chain A: E.250, G.273, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.73 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: R.543, N.751 Ligands: NAG-NAG-BMA-BMA.8, NAG-NAG-BMA-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: T.33, P.72, N.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.73, B:N.73 NAG-NAG.16: 3 residues within 4Å: Chain C: C.750, N.751 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.67, T.69, Q.288 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.288 Hydrogen bonds: C:Q.288, C:Q.288 NAG-NAG.20: 3 residues within 4Å: Chain C: E.250, G.273, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.73 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain D: N.751 Ligands: NAG-NAG-BMA-BMA.22 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain D: T.33, P.72, N.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.73, D:N.73

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-GAL-MAN-NAG.3: 14 residues within 4Å: Chain A: S.155, R.158, D.162, Q.165, R.194, Y.195, N.378, T.380, N.381, T.385, P.407, A.408, S.409, G.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158, A:R.158, A:R.194, A:S.409

5 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.5: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain B: N.67, T.69, Q.288 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.288 NAG-NAG-BMA.12: 1 residues within 4Å: Chain B: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 1 residues within 4Å: Chain C: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 3 residues within 4Å: Chain D: N.67, T.69, Q.288 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- BMA: beta-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-BMA.8: 7 residues within 4Å: Chain B: R.543, N.546, L.729, T.730, S.731 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.22: 5 residues within 4Å: Chain D: R.543, N.546, L.729, T.730 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN-NAG.10: 15 residues within 4Å: Chain B: N.378, T.380, N.381, T.385 Chain G: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, D.208, G.227, R.228 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.100 NAG-NAG-BMA-MAN-NAG-MAN-NAG.17: 12 residues within 4Å: Chain C: R.158, L.161, D.162, R.194, N.378, T.380, N.381, T.385, W.405, A.408, S.409, G.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-NAG.24: 11 residues within 4Å: Chain D: N.378, T.380, N.381, T.385 Chain E: Y.12, P.13, T.15, D.16, G.98, L.99, R.228 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.13: 6 residues within 4Å: Chain B: G.273, V.274, N.275, L.394, K.395, E.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 6 residues within 4Å: Chain D: G.273, V.274, N.275, L.394, K.395, E.396 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.396

4 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.29: 13 residues within 4Å: Chain A: K.531, P.532, F.533, M.534, L.783, Q.786, L.791 Chain D: I.519, P.532, S.761, K.762, G.763 Ligands: 2J9.55 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.791, D:P.532 2J9.40: 15 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Chain C: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Ligands: 2J9.46 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.532, B:T.535 Halogen bonds: C:M.534 2J9.46: 13 residues within 4Å: Chain B: I.519, P.532, S.761, K.762, G.763 Chain C: K.531, P.532, F.533, M.534, L.783, Q.786, L.791 Ligands: 2J9.40 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.786, C:L.791, B:P.532 2J9.55: 15 residues within 4Å: Chain A: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain D: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Ligands: 2J9.29 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.535, A:P.532 Halogen bonds: A:M.534

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.30: 10 residues within 4Å: Chain A: Y.488, P.516, L.517, A.518, R.523, V.685, G.688, A.689, T.690, E.738 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:Y.488, A:V.685 Hydrogen bonds: A:P.516, A:A.518, A:A.689, A:T.690, A:E.738, A:E.738 Salt bridges: A:R.523 GLU.41: 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 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.488, B:V.685 Hydrogen bonds: B:A.518, B:A.689, B:T.690, B:T.690, B:N.721, B:E.738, B:E.738, B:Y.764, E.41, E.41 Salt bridges: B:R.523 GLU.47: 10 residues within 4Å: Chain C: Y.488, P.516, L.517, A.518, R.523, V.685, G.688, A.689, T.690, E.738 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:Y.488, C:V.685 Hydrogen bonds: C:P.516, C:A.518, C:A.689, C:T.690, C:E.738, C:E.738 Salt bridges: C:R.523 GLU.56: 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 13 PLIP interactions: 11 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.488, D:V.685 Hydrogen bonds: D:A.518, D:A.689, D:T.690, D:T.690, D:N.721, D:E.738, D:E.738, D:Y.764, E.56, E.56 Salt bridges: D:R.523

14 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.31: 15 residues within 4Å: Chain A: N.549, G.551, F.553, L.556, P.561, W.564, V.567, L.568, L.619, M.620, V.826 Chain D: G.638, F.642 Ligands: POV.32, POV.33 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.553, A:F.553, A:L.556, A:L.556, A:W.564, A:W.564, A:W.564, A:V.567, A:L.568, A:L.568, A:L.619, A:V.826, D:F.642, D:F.642, D:F.642 Hydrogen bonds: A:F.553 POV.32: 10 residues within 4Å: Chain A: V.552, F.553, I.825, V.826, A.828, A.829, L.833 Ligands: POV.31, POV.33, CLR.35 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.553, A:F.553, A:I.825, A:V.826, A:A.828, A:A.829, A:L.833 POV.33: 9 residues within 4Å: Chain A: M.565, L.568, L.569, L.572, F.612, V.616 Ligands: POV.31, POV.32, POV.39 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.569, A:L.572, A:F.612, A:V.616 POV.38: 9 residues within 4Å: Chain A: K.870, C.871, Q.872 Chain D: F.579, R.583, L.608, Y.844, K.848 Ligands: CLR.52 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.579, D:L.608, A:K.870 Hydrogen bonds: D:Y.844 POV.39: 12 residues within 4Å: Chain A: C.576, F.579, V.580, R.583, T.607, L.608, L.609, F.612 Chain B: K.870, C.871 Ligands: POV.33, CLR.34 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.579, A:V.580, A:L.609, A:F.612 Salt bridges: A:R.583 POV.42: 10 residues within 4Å: Chain A: G.638, F.642 Chain B: F.553, L.556, W.564, L.568, M.620, I.648, V.826 Ligands: POV.43 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.642, A:F.642, B:F.553, B:L.556, B:L.556, B:W.564, B:W.564, B:W.564, B:L.568, B:I.648, B:V.826 POV.43: 12 residues within 4Å: Chain A: I.635, I.639 Chain B: V.552, F.553, W.613, V.616, V.826, A.828, A.829, L.833 Ligands: CLR.37, POV.42 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.613, B:V.616, B:V.826, B:A.829, B:L.833, A:I.635 POV.45: 9 residues within 4Å: Chain B: F.579, R.583, L.608, Y.844, K.848 Chain C: K.870, C.871, Q.872 Ligands: CLR.36 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.608, C:K.870 Hydrogen bonds: B:Y.844 POV.48: 17 residues within 4Å: Chain B: G.638, I.639, F.642 Chain C: N.549, G.551, F.553, L.556, P.561, W.564, V.567, L.568, V.616, L.619, M.620, V.826 Ligands: POV.49, POV.50 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.553, C:F.553, C:L.556, C:L.556, C:P.561, C:W.564, C:W.564, C:W.564, C:V.567, C:L.568, C:L.568, C:V.616, C:L.619, C:V.826, B:I.639, B:F.642, B:F.642, B:F.642, B:F.642 Hydrogen bonds: C:F.553 POV.49: 11 residues within 4Å: Chain B: I.639 Chain C: F.553, V.826, A.828, A.829, G.830, L.831, L.833 Ligands: POV.48, POV.50, CLR.51 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.553, C:F.553, C:V.826, C:A.828, C:A.829, C:L.831, C:L.833, B:I.639 POV.50: 9 residues within 4Å: Chain C: M.565, L.568, L.569, L.572, F.612, V.616 Ligands: POV.48, POV.49, POV.54 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.569, C:L.572, C:F.612, C:V.616 POV.54: 12 residues within 4Å: Chain C: C.576, F.579, V.580, R.583, T.607, L.608, L.609, F.612 Chain D: K.870, C.871 Ligands: CLR.44, POV.50 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.579, C:V.580, C:L.608, C:L.609, C:F.612 Salt bridges: C:R.583 POV.57: 10 residues within 4Å: Chain C: G.638, I.639, F.642 Chain D: F.553, L.556, W.564, L.568, M.620, I.648 Ligands: POV.58 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.553, D:L.556, D:L.556, D:W.564, D:W.564, D:L.568, D:I.648, C:I.639, C:F.642, C:F.642 POV.58: 11 residues within 4Å: Chain C: I.635, I.639 Chain D: V.552, F.553, W.613, V.616, V.826, A.828, A.829, L.833 Ligands: POV.57 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.635, D:W.613, D:V.616, D:V.826, D:A.828, D:A.829, D:L.833

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.34: 5 residues within 4Å: Chain A: G.840, E.841, Y.844 Chain D: Y.587 Ligands: POV.39 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.587, A:E.841, A:Y.844, A:Y.844 CLR.35: 5 residues within 4Å: Chain A: V.817, F.824, A.828 Chain D: Y.566 Ligands: POV.32 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.817, A:F.824, A:A.828, D:Y.566 CLR.36: 6 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.609, E.841, Y.844 Ligands: POV.45 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.609, B:E.841, B:Y.844, A:L.631 CLR.37: 5 residues within 4Å: Chain A: Y.566, L.569 Chain B: V.817, F.824 Ligands: POV.43 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.817, B:F.824, A:Y.566 CLR.44: 5 residues within 4Å: Chain B: Y.587 Chain C: G.840, E.841, Y.844 Ligands: POV.54 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.587, B:Y.587, C:E.841, C:Y.844, C:Y.844 CLR.51: 5 residues within 4Å: Chain B: Y.566 Chain C: V.817, F.824, A.828 Ligands: POV.49 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.817, C:F.824, C:A.828, B:Y.566 CLR.52: 6 residues within 4Å: Chain C: Y.587, L.631 Chain D: L.609, E.841, Y.844 Ligands: POV.38 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.631, D:L.609, D:E.841, D:Y.844 CLR.53: 5 residues within 4Å: Chain C: Y.566, L.569 Chain D: V.817, F.824, I.825 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.817, D:F.824, D:I.825, C:Y.566

4 x ZN: ZINC ION(Non-covalent)

ZN.59: 5 residues within 4Å: Chain E: E.8, D.10, D.19, H.24 Ligands: CA.60 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.8, E:E.8, E:D.10, E:D.19, E:H.24 ZN.61: 4 residues within 4Å: Chain F: E.8, D.10, D.19, H.24 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.8, F:D.10, F:D.19, F:D.19, F:H.24 ZN.63: 5 residues within 4Å: Chain G: E.8, D.10, D.19, H.24 Ligands: CA.64 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.8, G:E.8, G:D.10, G:D.19, G:H.24 ZN.65: 4 residues within 4Å: Chain H: E.8, D.10, D.19, H.24 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.8, H:D.10, H:D.19, H:D.19, H:H.24

4 x CA: CALCIUM ION(Non-covalent)

CA.60: 8 residues within 4Å: Chain E: E.8, D.10, N.14, D.19, D.208, R.228, L.230 Ligands: ZN.59 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.10, E:D.19 CA.62: 4 residues within 4Å: Chain F: D.10, Y.12, N.14, D.19 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.10, F:D.10, F:Y.12 CA.64: 7 residues within 4Å: Chain G: E.8, D.10, N.14, D.19, R.228, L.230 Ligands: ZN.63 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.10, G:D.19 CA.66: 4 residues within 4Å: Chain H: D.10, Y.12, N.14, D.19 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.10, H:D.10, H:Y.12

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
Concanavalin A: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

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

Concanavalin A

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