SMTL ID : 8bhg.1

GABA-A receptor a5 heteromer - a5V2 - Bretazenil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-4-1-mer

Ligands

5 x QMU: Bretazenil(Non-covalent)

QMU.1: 17 residues within 4Å: Chain A: F.103, H.105, S.162, Y.163, T.208, S.209, T.210, Y.213, I.215 Chain E: D.47, M.48, Y.49, F.68, F.69, A.70, T.133, V.183 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:T.210, A:Y.213 pi-Stacking: A:Y.213, E:F.68 Hydrogen bonds: E:T.133 QMU.5: 18 residues within 4Å: Chain A: D.47, M.48, Y.49, F.68, F.69, A.70, L.131, T.133 Chain B: F.112, R.114, S.170, S.171, Y.172, T.215, T.216, S.217, Y.220, V.222 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.49, B:Y.220 Hydrogen bonds: A:T.133 pi-Stacking: A:F.68, B:Y.220 QMU.6: 20 residues within 4Å: Chain B: D.56, M.57, Y.58, F.77, F.78, A.79, M.130, L.140, T.142, K.184, E.189 Chain C: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:D.56, B:Y.58, B:Y.58, B:A.79, C:T.210 Hydrogen bonds: B:T.142 pi-Stacking: B:F.77, B:F.77, C:Y.213 QMU.14: 17 residues within 4Å: Chain D: D.47, M.48, Y.49, F.68, F.69, A.70, L.131, T.133 Chain E: F.103, H.105, S.162, Y.163, T.208, S.209, T.210, Y.213, I.215 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:Y.49, E:F.103, E:T.210, E:Y.213 Hydrogen bonds: D:T.133 pi-Stacking: D:F.68, D:F.68, E:Y.213 QMU.15: 17 residues within 4Å: Chain C: D.47, M.48, Y.49, F.68, F.69, A.70, T.133 Chain D: F.103, H.105, S.162, Y.163, I.206, T.208, S.209, T.210, Y.213, I.215 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:D.47, D:F.103, D:T.210, D:Y.213 Hydrogen bonds: C:T.133 pi-Stacking: C:F.68, D:Y.213

5 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.2: 12 residues within 4Å: Chain A: T.59, T.271, I.274, S.275, N.278, S.279 Chain B: I.281, N.285 Chain E: T.271, S.275 Ligands: DMU.7, DMU.18 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:I.274, E:T.271 Hydrogen bonds: A:S.275, A:N.278, B:N.285, B:N.285 DMU.7: 16 residues within 4Å: Chain A: T.268, T.271, L.272, S.275 Chain B: L.274, T.277, T.278, I.281, S.282, N.285, S.286 Chain C: I.274, N.278, K.282 Ligands: DMU.2, DMU.11 10 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:N.278, C:N.278, B:S.282, B:N.285, B:S.286, B:S.286 Hydrophobic interactions: B:L.274, B:I.281, A:T.268, A:L.272 DMU.11: 17 residues within 4Å: Chain B: T.275, T.278, L.279, S.282 Chain C: T.59, L.267, T.270, T.271, I.274, S.275, N.278, S.279 Chain D: I.274, N.278, K.282 Ligands: DMU.7, DMU.16 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.270, C:I.274, C:I.274 Hydrogen bonds: C:N.278, C:S.279, D:N.278 DMU.16: 17 residues within 4Å: Chain C: T.268, T.271, L.272, S.275 Chain D: T.59, L.267, T.270, T.271, I.274, S.275, N.278, S.279 Chain E: I.274, N.278, K.282 Ligands: DMU.11, DMU.18 8 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: C:T.271, C:L.272, D:T.270, D:I.274 Hydrogen bonds: E:N.278, D:N.278, D:S.279, D:S.279 DMU.18: 16 residues within 4Å: Chain A: I.274, N.278 Chain D: T.268, T.271, L.272, S.275 Chain E: T.59, L.267, T.270, T.271, I.274, S.275, N.278, S.279 Ligands: DMU.2, DMU.16 9 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:T.271, E:I.274, E:I.274, D:T.268, D:T.271, D:L.272 Hydrogen bonds: E:N.278, E:S.279, A:N.278

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 7 residues within 4Å: Chain A: G.54, P.55, V.56, L.191, N.192, Q.193, Y.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.54, A:V.56, A:N.192, A:Q.193, A:Q.193 NO3.8: 7 residues within 4Å: Chain B: P.64, V.65, R.197, L.198, Y.199, Q.200, F.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.65, B:Y.199 NO3.12: 6 residues within 4Å: Chain C: P.55, V.56, L.191, N.192, Q.193, Y.194 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.56, C:N.192, C:Q.193, C:Q.193

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

NAG.4: 3 residues within 4Å: Chain A: N.167, E.204, N.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.205 NAG.9: 8 residues within 4Å: Chain B: W.183, K.184, R.185, S.187, V.188, N.208, T.209, T.210 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.184, B:S.187, B:S.187, B:S.187 NAG.10: 1 residues within 4Å: Chain B: N.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.90 NAG.13: 5 residues within 4Å: Chain C: N.167, V.171, T.203, E.204, N.205 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain D: V.171, N.205 No protein-ligand interaction detected (PLIP) NAG.19: 5 residues within 4Å: Chain E: N.167, T.203, E.204, N.205, E.212 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.167

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

2023-11-15

Peptides

Gamma-aminobutyric acid receptor subunit alpha-5: ACDE
Gamma-aminobutyric acid receptor subunit gamma-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

B
B

Membrane

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

Gamma-aminobutyric acid receptor subunit gamma-2