SMTL ID : 6hup.1

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with diazepam (Valium), GABA and megabody Mb38.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.1: 7 residues within 4Å: Chain A: N.146, T.148 Chain B: K.137 Chain C: D.159, W.162 Chain D: K.152 Ligands: NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP)

3 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 B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: S.226, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain E: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.3: 8 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN-MAN.7: 8 residues within 4Å: Chain E: N.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.217

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.5: 7 residues within 4Å: Chain D: L.124, N.146, M.149, P.150 Chain E: D.114, Q.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.115, E:D.114

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.8: 12 residues within 4Å: Chain A: R.284, T.341, F.345, K.347, R.348, F.421, N.422, S.423, S.425, K.426, I.427, L.430 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.341, A:I.427, A:L.430 Hydrogen bonds: A:R.284, A:S.423, A:K.426 Salt bridges: A:R.284, A:K.347, A:K.347, A:R.348, A:K.426 PIO.12: 10 residues within 4Å: Chain D: R.284, T.341, F.345, R.348, N.422, S.423, S.425, K.426, I.427, L.430 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.341, D:I.427 Hydrogen bonds: D:R.284, D:S.423, D:S.423, D:S.425, D:K.426 Salt bridges: D:R.284, D:R.348

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

ABU.9: 10 residues within 4Å: Chain A: F.100, R.102, T.165 Chain B: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.182, B:F.225, B:Y.230 Hydrogen bonds: B:Y.122, B:S.181, A:T.165 Salt bridges: A:R.102 ABU.13: 9 residues within 4Å: Chain D: F.100, R.102, T.165 Chain E: Y.122, E.180, S.181, Y.182, T.227, Y.230 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.182, E:Y.230, D:F.100 Hydrogen bonds: E:Y.122, E:S.181, E:T.227, D:T.165 Salt bridges: D:R.102

3 x DZP: 7-CHLORO-1-METHYL-5-PHENYL-1,3-DIHYDRO-2H-1,4-BENZODIAZEPIN-2-ONE(Non-covalent)

DZP.10: 11 residues within 4Å: Chain A: I.263, L.267, P.268, M.271, T.272 Chain B: M.286, T.287, N.290, L.310, M.311, F.314 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.287, B:L.310, B:F.314, B:F.314, A:P.268 DZP.11: 12 residues within 4Å: Chain C: Y.97, N.99, F.116 Chain D: F.135, H.137, S.194, Y.195, V.238, Q.239, S.240, S.241, Y.245 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.135, D:F.135, D:Y.195, D:V.238, D:Y.245, D:Y.245, C:Y.97, C:F.116 Hydrogen bonds: D:S.240, D:S.241 Halogen bonds: D:H.137 DZP.14: 11 residues within 4Å: Chain D: I.263, L.267, P.268, M.271, L.304 Chain E: M.286, T.287, N.290, L.310, M.311, F.314 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:T.287, E:L.310, E:F.314, E:F.314, D:P.268, D:L.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Masiulis, S. et al., GABAAreceptor signalling mechanisms revealed by structural pharmacology. Nature (2019)

Release Date

2019-01-02

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Gamma-aminobutyric acid receptor subunit gamma-2: C
Megabody Mb38: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
G

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit gamma-2

Megabody Mb38

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