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Human gabaa receptor ALPHA1-BETA2-GAMMA2 subtype in complex with GABA plus flumazenil

Analyse Human gabaa receptor ALPHA1-BETA2-GAMMA2 subtype in complex with GABA plus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X3U
Type: protein
Length: 2,121 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-aminobutyric acid receptor subunit beta-2; Gamma-aminobutyric acid receptor subunit…
UniProt: P47870, P14867, P18507
Ligands: ABU, FYP, NAG, MAN, BMA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 7 distinct chains · 25% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Gamma-aminobutyric acid receptor subunit beta-2	protein	334	35% helix, 31% strand	P47870
B, D	Gamma-aminobutyric acid receptor subunit alpha-1	protein	338	36% helix, 30% strand	P14867
E	Gamma-aminobutyric acid receptor subunit gamma-2	protein	333	35% helix, 31% strand	P18507
I	Kappa Fab light chain	protein	105	0% helix, 44% strand	—
J	IGG2B Fab heavy chain	protein	116	3% helix, 48% strand	—
L	Kappa Fab light chain	protein	106	0% helix, 46% strand	—
K	IGG2B Fab heavy chain	protein	117	0% helix, 51% strand	—

Ligands and binding sites

ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains A, B, C, D
FYP · Ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1, 5-a][1,4]benzodiazepine-3-carboxylate · ligand · chains D, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, E, D
MAN · alpha-D-mannopyranose · sugar · 7 copies · chains E, D
BMA · beta-D-mannopyranose · sugar · 3 copies · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	733	0.84	0.87	90	empty
2	762	0.73	0.79	58	empty
3	705	0.73	0.79	56	empty
4	154	0.72	0.90	32	empty
5	152	0.71	0.90	24	empty

Interfaces

11 interfaces between chains.

A–B · 2849 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2757 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 2474 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 2436 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 2406 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

6X3U · Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus flumazenil · the same entry in another collection · chain K against K, TM-score 1.00
P47870 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-2… · a predicted model of the same protein · chain C against A, TM-score 0.98
P18507 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit gamma-2… · a predicted model of the same protein · chain E against A, TM-score 0.98
P14867 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-1… · a predicted model of the same protein · chain B against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P47870
Every structure of UniProt P14867
Every structure of UniProt P18507
Elsewhere: RCSB PDB 6X3U · PDBe 6X3U · UniProt P47870 · UniProt P14867 · UniProt P18507

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