- Coordinates
- PDB Format
- 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
- 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:7 interactions with chain D, 3 Ligand-Ligand interactions- Hydrophobic interactions: D:Y.488
- Hydrogen bonds: D:P.516, D:A.518, D:A.689, D:T.690, D:E.738, E.29, E.29, E.29
- 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 PLIPNAG.13: 2 residues within 4Å:- Chain A: P.72, N.73
Ligand excluded by PLIPNAG.14: 3 residues within 4Å:- Chain A: N.423, I.424, T.425
Ligand excluded by PLIPNAG.15: 3 residues within 4Å:- Chain A: R.543, C.750, N.751
Ligand excluded by PLIPNAG.17: 2 residues within 4Å:- Chain B: N.67, T.69
Ligand excluded by PLIPNAG.18: 2 residues within 4Å:- Chain B: P.72, N.73
Ligand excluded by PLIPNAG.19: 4 residues within 4Å:- Chain B: N.378, T.380, N.381, T.385
Ligand excluded by PLIPNAG.20: 1 residues within 4Å:- Chain B: N.412
Ligand excluded by PLIPNAG.21: 7 residues within 4Å:- Chain B: R.543, P.545, N.546, L.729, T.730, S.731, D.732
Ligand excluded by PLIPNAG.23: 2 residues within 4Å:- Chain C: N.67, T.69
Ligand excluded by PLIPNAG.24: 1 residues within 4Å:- Chain C: N.73
Ligand excluded by PLIPNAG.25: 2 residues within 4Å:- Chain C: N.412, T.414
Ligand excluded by PLIPNAG.26: 2 residues within 4Å:- Chain C: N.423, T.425
Ligand excluded by PLIPNAG.27: 2 residues within 4Å:- Chain C: R.543, N.546
Ligand excluded by PLIPNAG.28: 3 residues within 4Å:- Chain C: R.748, N.749, N.751
Ligand excluded by PLIPNAG.30: 2 residues within 4Å:- Chain D: N.67, R.68
Ligand excluded by PLIPNAG.31: 1 residues within 4Å:- Chain D: N.73
Ligand excluded by PLIPNAG.32: 2 residues within 4Å:- Chain D: S.429, N.430
Ligand excluded by PLIPNAG.33: 3 residues within 4Å:- Chain D: K.544, N.546
- Ligands: NAG.34
Ligand excluded by PLIPNAG.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
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- 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
- 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
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x GLU: GLUTAMIC ACID(Non-covalent)
- 20 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.