SMTL ID : 8bgi.1

GABA-A receptor a5 homomer - a5V1 - Flumazenil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-pentamer

Ligands

29 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: R.190, L.191, Y.194, H.195, K.225 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: R.252, K.326 Chain B: K.315 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: P.55, V.56, L.191, N.192, Q.193, Y.194 Ligand excluded by PLIP SO4.4: 9 residues within 4Å: Chain A: H.113, G.114, M.115, N.119, R.135 Chain B: F.103, F.104, D.107, S.110 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: K.74, D.127, R.129 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: K.225, I.226, G.227 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.190, L.191, H.195, K.225 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: R.252, A.322, K.326 Chain C: K.315 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain B: P.55, V.56, L.191, N.192, Q.193, Y.194 Ligand excluded by PLIP SO4.13: 9 residues within 4Å: Chain B: H.113, G.114, M.115, N.119, R.135 Chain C: F.103, F.104, D.107, S.110 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: K.74, D.127, R.129 Ligands: NAG.19 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: K.225, I.226, G.227 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: R.40, Q.43, R.45, W.73, K.74, R.129 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: R.190, L.191, Y.194, H.195, K.225 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: R.252, A.322, K.326 Chain D: K.315 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: P.55, V.56, L.191, N.192, Q.193, Y.194 Ligand excluded by PLIP SO4.24: 9 residues within 4Å: Chain C: H.113, G.114, M.115, N.119, R.135 Chain D: F.103, F.104, D.107, S.110 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: R.224, K.225, I.226, G.227 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: R.190, L.191, H.195, K.225 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain D: R.252, K.326 Chain E: K.315 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain D: P.55, V.56, L.191, N.192, Q.193, Y.194 Ligand excluded by PLIP SO4.32: 9 residues within 4Å: Chain D: H.113, G.114, M.115, N.119, R.135 Chain E: F.103, F.104, D.107, S.110 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: K.225, I.226, G.227 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: R.190, L.191, H.195, K.225 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain A: K.315 Chain E: R.252, K.326 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain E: P.55, V.56, L.191, N.192, Q.193, Y.194 Ligand excluded by PLIP SO4.41: 9 residues within 4Å: Chain A: F.103, F.104, D.107, S.110 Chain E: H.113, G.114, M.115, N.119, R.135 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain A: A.284 Chain E: K.225, I.226, G.227 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain E: E.153, M.197, H.221, L.222, K.223 Ligand excluded by PLIP

5 x FYP: ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate(Non-covalent)

FYP.7: 17 residues within 4Å: Chain A: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213, I.215 Chain E: D.47, M.48, Y.49, F.68, A.70, M.121, T.133 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.103, A:F.103, A:I.206, A:T.208, A:Y.213, E:Y.49 pi-Stacking: A:Y.163, A:Y.213 Hydrogen bonds: E:T.133 FYP.17: 15 residues within 4Å: Chain A: D.47, M.48, Y.49, F.68, A.70, T.133 Chain B: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.103, B:T.208, A:Y.49 pi-Stacking: B:Y.213 Hydrogen bonds: A:T.133 FYP.26: 17 residues within 4Å: Chain B: D.47, M.48, Y.49, F.68, A.70, T.133, T.179, V.183 Chain C: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.103, C:T.208, B:Y.49 pi-Stacking: C:Y.213 Hydrogen bonds: B:T.133 FYP.34: 15 residues within 4Å: Chain C: D.47, M.48, Y.49, F.68, A.70, T.133 Chain D: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.49, D:Y.213, D:Y.213 Hydrogen bonds: C:T.133 pi-Stacking: D:F.103 FYP.37: 15 residues within 4Å: Chain D: D.47, Y.49, F.68, A.70, T.133, V.183 Chain E: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.103, E:T.208, D:Y.49 pi-Stacking: E:Y.213 Hydrogen bonds: D:T.133

5 x P9N: Pregnanolone(Non-covalent)

P9N.8: 11 residues within 4Å: Chain A: F.301, I.305, A.308, T.309, Y.312 Chain E: I.242, Q.245, V.246, W.249, R.329, P.333 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:I.305, A:A.308, A:Y.312, E:I.242, E:V.246, E:W.249, E:W.249, E:W.249 Hydrogen bonds: E:R.329 P9N.18: 11 residues within 4Å: Chain A: I.242, Q.245, V.246, F.248, W.249, P.333 Chain B: F.301, I.305, A.308, T.309, Y.312 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.242, A:V.246, A:W.249, A:W.249, A:W.249, B:I.305, B:A.308, B:Y.312 Water bridges: A:Q.245 P9N.27: 11 residues within 4Å: Chain B: I.242, Q.245, V.246, W.249, R.329, P.333 Chain C: F.301, I.305, A.308, T.309, Y.312 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.242, B:V.246, B:W.249, B:W.249, B:W.249, B:W.249, C:A.308 Hydrogen bonds: B:R.329 P9N.35: 10 residues within 4Å: Chain C: I.242, Q.245, V.246, W.249, P.333 Chain D: F.301, I.305, A.308, T.309, Y.312 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:A.308, D:Y.312, C:I.242, C:V.246, C:W.249, C:W.249, C:W.249, C:W.249 Hydrogen bonds: C:Q.245 P9N.44: 10 residues within 4Å: Chain D: I.242, Q.245, V.246, W.249, P.333 Chain E: F.301, I.305, A.308, T.309, Y.312 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.242, D:V.246, D:W.249, D:W.249, D:W.249, E:A.308, E:Y.312 Hydrogen bonds: D:Q.245 Water bridges: D:W.249

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

NAG.9: 3 residues within 4Å: Chain A: N.167, V.171, N.205 No protein-ligand interaction detected (PLIP) NAG.19: 6 residues within 4Å: Chain B: R.45, T.72, R.129, N.176, S.178 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.72, B:N.176 NAG.20: 4 residues within 4Å: Chain B: N.167, T.203, E.204, N.205 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain C: N.167, V.171, N.205, T.214 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.205 NAG.36: 4 residues within 4Å: Chain D: N.167, V.171, N.205, T.214 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.205 NAG.45: 4 residues within 4Å: Chain E: N.167, T.203, E.204, N.205 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.167, E:N.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., The molecular basis of drug selectivity for alpha 5 subunit-containing GABA A receptors. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-11-08

Peptides

Gamma-aminobutyric acid receptor subunit alpha-5: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-5