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

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: 6D6T
Type: protein
Length: 2,082 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
Ligands: Y01, ABU, FYP, NAG, MAN, BMA
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 28% helix, 34% 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, 31% strand	P47870
B	Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1	protein	333	37% helix, 30% strand	P14867
D	Gamma-aminobutyric acid receptor subunit alpha-1,GAMMA- aminobutyric acid receptor subunit alpha-1	protein	337	38% helix, 30% strand	P14867
E	Human GABA-a receptor subunit gamma-2	protein	302	28% helix, 33% strand	—
I, L	Kappa Fab light chain	protein	106	0% helix, 47% strand	—
J	IGG2B Fab heavy chain	protein	116	5% helix, 48% strand	—
K	IGG2B Fab heavy chain	protein	116	3% helix, 47% 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 · 11 copies · chains A, B, C, D, E
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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	775	0.85	0.88	94	empty
2	1036	0.79	0.80	97	empty
3	647	0.73	0.80	77	empty
4	72	0.72	0.97	22	empty
5	567	0.72	0.80	58	FYP

Interfaces

13 interfaces between chains.

A–B · 2750 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2544 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 2394 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 2151 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1815 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

6D6T · 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 D 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 C against A, TM-score 0.96

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
Elsewhere: RCSB PDB 6D6T · PDBe 6D6T · UniProt P47870 · UniProt P14867

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