SMTL ID : 5ojm.1

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-5-5-mer

Ligands

3 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.1: 11 residues within 4Å: Chain A: N.180, R.223, V.225, S.226, R.227, S.240, S.242 Chain F: N.30, Y.31, S.103, D.113 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.113, A:R.223, A:R.227, A:S.240 NAG-NAG-BMA-MAN-MAN.2: 11 residues within 4Å: Chain B: N.180, E.221, R.223, S.226, R.227, S.240, S.242, R.244 Chain G: N.30, Y.31, D.113 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:R.223, B:R.227, B:S.240, G:Y.31, G:D.113, G:D.113 NAG-NAG-BMA-MAN-MAN.3: 11 residues within 4Å: Chain C: N.180, R.223, S.226, R.227, S.240, S.242, F.243, R.244 Chain H: N.30, Y.31, D.113 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:R.223, C:R.227, C:S.240, H:D.113

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.4: 9 residues within 4Å: Chain D: N.180, R.223, S.226, R.227, S.242, R.244 Chain I: N.30, Y.31, D.113 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D Hydrogen bonds: I:Y.31, I:D.113, D:R.223 NAG-NAG-BMA-MAN-MAN-MAN.5: 11 residues within 4Å: Chain E: N.180, R.223, V.225, S.226, R.227, S.240, S.242 Chain J: N.30, Y.31, Y.112, D.113 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain E Hydrogen bonds: J:D.113, E:R.223, E:R.227, E:S.240

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

NAG.6: 2 residues within 4Å: Chain A: N.111, H.150 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.111, H.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.111 NAG.8: 2 residues within 4Å: Chain C: N.111, H.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.111 NAG.9: 2 residues within 4Å: Chain D: N.111, H.150 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.111 NAG.10: 3 residues within 4Å: Chain E: L.110, N.111, H.150 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, P.S. et al., Structural basis for GABAA receptor potentiation by neurosteroids. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-10-04

Peptides

Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5: ABCDE
Nanobody Nb25: FGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
K

G
L

H
M

I
N

J
O

Membrane

We predict this structure to be a membrane protein.
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Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5

Nanobody Nb25

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