SMTL ID : 6d6t.1

Human GABA-A receptor alpha1-beta2-gamma2 subtype in complex with GABA and flumazenil, conformation B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.86 Å

Oligo State

hetero-2-2-1-2-2-mer

Ligands

2 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.1: 5 residues within 4Å: Chain A: N.149, I.194, K.196, S.211, K.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.192, A:K.192, A:K.196 NAG-NAG-BMA.3: 5 residues within 4Å: Chain C: N.149, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.196

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN.2: 8 residues within 4Å: Chain B: N.111 Chain D: K.117 Chain E: S.137, N.138, G.141, D.157, W.160 Ligands: NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.117

1 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

NAG-NAG-BMA-MAN-MAN.4: 3 residues within 4Å: Chain D: N.111, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.16: 2 residues within 4Å: Chain C: N.80, H.119 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.80 NAG.22: 4 residues within 4Å: Chain E: R.222, S.223, S.224, N.245 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.224, E:S.224

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.6: 6 residues within 4Å: Chain A: Y.157, F.200, T.202, Y.205 Chain B: F.65, R.67 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.157, A:Y.205, B:F.65 Hydrogen bonds: A:Y.97, A:S.156, A:T.202 Salt bridges: B:R.67 ABU.17: 8 residues within 4Å: Chain C: Y.157, F.200, T.202, Y.205 Chain D: F.65, R.67, L.118, T.130 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.65, C:Y.157, C:Y.205 Hydrogen bonds: D:T.130, C:Y.205 Salt bridges: D:R.67

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 5 residues within 4Å: Chain A: M.294, W.319, F.323, F.324, V.327 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.319, A:F.323, A:V.327 Y01.8: 2 residues within 4Å: Chain A: W.241, R.321 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.241 Hydrogen bonds: A:S.329, A:S.329 Y01.9: 3 residues within 4Å: Chain A: L.231, L.235 Ligands: Y01.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.235 Y01.10: 4 residues within 4Å: Chain A: M.283, F.331, Y.338, Y.339 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.338 Y01.11: 3 residues within 4Å: Chain A: V.238, W.241 Ligands: Y01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.238, A:W.241 Y01.12: 5 residues within 4Å: Chain B: N.308, K.312 Chain C: I.242, A.246, A.249 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.242, C:A.246, C:A.249 Hydrogen bonds: B:K.312 Y01.13: 3 residues within 4Å: Chain B: V.227, I.235, W.341 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.227, B:V.227, B:I.235, B:W.341, B:W.341 Y01.14: 2 residues within 4Å: Chain B: I.228, L.232 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.228, B:L.232 Y01.15: 3 residues within 4Å: Chain B: L.324, A.328, L.332 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.324, B:A.328 Y01.19: 4 residues within 4Å: Chain D: G.224, I.228, L.232 Ligands: Y01.21 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.228, D:L.232 Y01.20: 3 residues within 4Å: Chain D: I.321, F.329, L.332 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.329, D:L.332 Y01.21: 4 residues within 4Å: Chain D: I.223, V.227, W.341 Ligands: Y01.19 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.227, D:W.341

1 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.18: 11 residues within 4Å: Chain D: H.102, Y.160, S.205, S.206, T.207, Y.210 Chain E: D.93, Y.95, F.114, A.116, T.179 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:Y.95, E:F.114 pi-Stacking: E:F.114, D:Y.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, S. et al., Structure of a human synaptic GABAAreceptor. Nature (2018)

Release Date

2018-06-27

Peptides

Gamma-aminobutyric acid receptor subunit beta-2,Gamma-aminobutyric acid receptor subunit beta-2: AC
Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1: BD
Human GABA-A receptor subunit gamma-2: E
Kappa Fab Light Chain: FH
IgG2b Fab Heavy Chain: GI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
I

H
L

G
J

I
K

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Gamma-aminobutyric acid receptor subunit beta-2,Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1

Human GABA-A receptor subunit gamma-2

Kappa Fab Light Chain

IgG2b Fab Heavy Chain

Related Entries With Identical Sequence