- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-pentamer
- 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
- 5 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: 3 residues within 4Å:- Chain A: P.132, N.134, H.173
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 3 residues within 4Å:- Chain B: P.132, N.134, H.173
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 3 residues within 4Å:- Chain C: P.132, N.134, H.173
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 3 residues within 4Å:- Chain D: P.132, N.134, H.173
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 3 residues within 4Å:- Chain E: P.132, N.134, H.173
No protein-ligand interaction detected (PLIP)- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.11: 4 residues within 4Å:- Chain A: N.62, S.64, F.65, E.68
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.62, A:E.68
NAG.21: 4 residues within 4Å:- Chain B: N.62, S.64, F.65, E.68
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.62, B:E.68
NAG.27: 4 residues within 4Å:- Chain C: N.62, S.64, F.65, E.68
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.62, C:E.68
NAG.34: 4 residues within 4Å:- Chain D: N.62, S.64, F.65, E.68
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:N.62, D:E.68
NAG.40: 4 residues within 4Å:- Chain E: N.62, S.64, F.65, E.68
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:N.62, E:E.68
- 5 x HSM: HISTAMINE(Non-covalent)
HSM.12: 9 residues within 4Å:- Chain A: Y.151, E.209, S.210, Y.211, F.254, Y.259
- Chain B: D.97, Y.116, Q.118
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:Y.116
- Hydrogen bonds: B:D.97, B:Q.118, A:Y.151, A:Y.151
- pi-Stacking: B:Y.116
HSM.17: 9 residues within 4Å:- Chain B: Y.151, E.209, S.210, Y.211, F.254, Y.259
- Chain C: D.97, Y.116, Q.118
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:Y.116
- Hydrogen bonds: C:D.97, C:Q.118, B:Y.151, B:Y.151
- pi-Stacking: C:Y.116
HSM.23: 9 residues within 4Å:- Chain C: Y.151, E.209, S.210, Y.211, F.254, Y.259
- Chain D: D.97, Y.116, Q.118
7 PLIP interactions:3 interactions with chain C, 4 interactions with chain D- Hydrogen bonds: C:Y.151, C:Y.151, D:D.97, D:Q.118
- Water bridges: C:Y.259
- Hydrophobic interactions: D:Y.116
- pi-Stacking: D:Y.116
HSM.29: 9 residues within 4Å:- Chain D: Y.151, E.209, S.210, Y.211, F.254, Y.259
- Chain E: D.97, Y.116, Q.118
7 PLIP interactions:4 interactions with chain E, 3 interactions with chain D- Hydrophobic interactions: E:Y.116
- Hydrogen bonds: E:D.97, E:Q.118, D:Y.151, D:Y.151
- pi-Stacking: E:Y.116
- Water bridges: D:Y.259
HSM.35: 9 residues within 4Å:- Chain A: D.97, Y.116, Q.118
- Chain E: Y.151, E.209, S.210, Y.211, F.254, Y.259
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain E- Hydrophobic interactions: A:Y.116
- Hydrogen bonds: A:D.97, A:Q.118, E:Y.151, E:Y.151
- pi-Stacking: A:Y.116
- Water bridges: E:Y.259
- 15 x D10: DECANE(Non-covalent)
D10.13: 6 residues within 4Å:- Chain A: I.288, W.291, W.295
- Chain E: L.351, F.355, Y.358
9 PLIP interactions:5 interactions with chain A, 4 interactions with chain E- Hydrophobic interactions: A:I.288, A:W.291, A:W.295, A:W.295, A:W.295, E:L.351, E:F.355, E:F.355, E:Y.358
D10.14: 2 residues within 4Å:- Chain A: W.295, R.375
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:W.295
D10.15: 6 residues within 4Å:- Chain A: I.284, W.291, P.379, S.383, N.386, W.390
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:W.291
D10.18: 6 residues within 4Å:- Chain A: L.351, F.355, Y.358
- Chain B: I.288, W.291, W.295
9 PLIP interactions:4 interactions with chain A, 5 interactions with chain B- Hydrophobic interactions: A:L.351, A:F.355, A:F.355, A:Y.358, B:I.288, B:W.291, B:W.295, B:W.295, B:W.295
D10.19: 2 residues within 4Å:- Chain B: W.295, R.375
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.295
D10.20: 6 residues within 4Å:- Chain B: I.284, W.291, P.379, S.383, N.386, W.390
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.291
D10.24: 6 residues within 4Å:- Chain B: L.351, F.355, Y.358
- Chain C: I.288, W.291, W.295
9 PLIP interactions:4 interactions with chain B, 5 interactions with chain C- Hydrophobic interactions: B:L.351, B:F.355, B:F.355, B:Y.358, C:I.288, C:W.291, C:W.295, C:W.295, C:W.295
D10.25: 2 residues within 4Å:- Chain C: W.295, R.375
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:W.295
D10.26: 6 residues within 4Å:- Chain C: I.284, W.291, P.379, S.383, N.386, W.390
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:W.291
D10.30: 6 residues within 4Å:- Chain C: L.351, F.355, Y.358
- Chain D: I.288, W.291, W.295
9 PLIP interactions:4 interactions with chain C, 5 interactions with chain D- Hydrophobic interactions: C:L.351, C:F.355, C:F.355, C:Y.358, D:I.288, D:W.291, D:W.295, D:W.295, D:W.295
D10.31: 2 residues within 4Å:- Chain D: W.295, R.375
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:W.295
D10.32: 6 residues within 4Å:- Chain D: I.284, W.291, P.379, S.383, N.386, W.390
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:W.291
D10.36: 6 residues within 4Å:- Chain D: L.351, F.355, Y.358
- Chain E: I.288, W.291, W.295
9 PLIP interactions:5 interactions with chain E, 4 interactions with chain D- Hydrophobic interactions: E:I.288, E:W.291, E:W.295, E:W.295, E:W.295, D:L.351, D:F.355, D:F.355, D:Y.358
D10.37: 2 residues within 4Å:- Chain E: W.295, R.375
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:W.295
D10.38: 6 residues within 4Å:- Chain E: I.284, W.291, P.379, S.383, N.386, W.390
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:W.291
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.16: 4 residues within 4Å:- Chain A: K.157, S.158
- Chain B: F.159, H.161
Ligand excluded by PLIPCL.22: 4 residues within 4Å:- Chain B: K.157, S.158
- Chain C: F.159, H.161
Ligand excluded by PLIPCL.28: 4 residues within 4Å:- Chain C: K.157, S.158
- Chain D: F.159, H.161
Ligand excluded by PLIPCL.33: 3 residues within 4Å:- Chain D: S.158
- Chain E: F.159, H.161
Ligand excluded by PLIPCL.39: 3 residues within 4Å:- Chain A: F.159, H.161
- Chain E: S.158
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mihaylov, D.B. et al., Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state. To Be Published
- Release Date
- 2025-06-04
- Peptides
- Gamma-aminobutyric acid receptor subunit beta-3: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-pentamer
- 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
- 5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 5 x HSM: HISTAMINE(Non-covalent)
- 15 x D10: DECANE(Non-covalent)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mihaylov, D.B. et al., Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state. To Be Published
- Release Date
- 2025-06-04
- Peptides
- Gamma-aminobutyric acid receptor subunit beta-3: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E - Membrane
-
We predict this structure to be a membrane protein.