Research workbench

Human GABA-a receptor ALPHA1-BETA2-GAMMA2 subtype in complex with GABA and flumazenil, conformation a

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

PDB: 6D6U
Type: protein
Length: 2,106 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: Y01, ABU, FYP, NAG, MAN, BMA
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 7 distinct chains · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Gamma-aminobutyric acid receptor subunit beta-2,GAMMA- aminobutyric acid receptor subunit beta-2	protein	333	36% helix, 29% strand	P47870
B	Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1	protein	336	36% helix, 26% strand	P14867
D	Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1	protein	338	37% helix, 26% strand	P14867
E	Gamma-aminobutyric acid receptor subunit gamma-2,GAMMA- aminobutyric acid receptor subunit gamma-2	protein	322	33% helix, 27% strand	P18507
I, L	Kappa Fab light chain	protein	106	0% helix, 46% strand	—
J	IGG2B Fab heavy chain	protein	116	5% helix, 47% strand	—
K	IGG2B Fab heavy chain	protein	116	3% helix, 49% strand	—

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, E, B, C, D
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 · 10 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 7 copies · chains E, D, B, C
BMA · beta-D-mannopyranose · sugar · 4 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.86	0.86	126	Y01
2	620	0.78	0.83	66	Y01
3	610	0.74	0.81	60	FYP
4	521	0.74	0.82	64	empty
5	743	0.72	0.78	56	empty

Interfaces

13 interfaces between chains.

C–D · 2764 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 2443 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 2093 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 2078 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1793 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

6D6U · Human GABA-A receptor alpha1-beta2-gamma2 subtype in complex with GABA and flumazenil… · the same entry in another collection · chain K against K, TM-score 1.00
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
P47870 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-2… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 6D6U · PDBe 6D6U · UniProt P47870 · UniProt P14867 · UniProt P18507

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.