MolNFT v1 · #152019 · protein

Cryo-EM structure of the human synaptic ALPHA1-BETA3-GAMMA2 gabaa receptor in complex with MEGABODY38 in a lipid nanodisc

6I53 · Gamma-aminobutyric acid receptor subunit beta-3: “Cryo-EM structure of the human synaptic ALPHA1-BETA3-GAMMA2 gabaa receptor in complex with MEGABODY38 in a…”. Electron microscopy, 5 ligands (POV, PIO, NAG), 20 pockets (best…

PDB: 6I53
Type: protein
Length: 1,821 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-aminobutyric acid receptor subunit beta-3; Gamma-aminobutyric acid receptor subunit…
UniProt: P28472, P14867, P18507
Ligands: POV, PIO, NAG, MAN, BMA
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 6 distinct chains · 31% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Gamma-aminobutyric acid receptor subunit beta-3	protein	336	36% helix, 28% strand	P28472
A	Gamma-aminobutyric acid receptor subunit alpha-1	protein	349	31% helix, 27% strand	P14867
B	Gamma-aminobutyric acid receptor subunit beta-3	protein	338	35% helix, 31% strand	P28472
C	Gamma-aminobutyric acid receptor subunit gamma-2	protein	328	32% helix, 33% strand	P18507
D	Gamma-aminobutyric acid receptor subunit alpha-1	protein	347	32% helix, 27% strand	P14867
G	MEGABODY38	protein	123	5% helix, 50% strand	—

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 3 copies · chains E, A, B, D
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 · ligand · 2 copies · chains A, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains E, A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 11 copies · chains E, C, B, A
BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, C, B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.86	0.86	113	empty
2	793	0.85	0.88	82	empty
3	525	0.68	0.78	70	empty
4	110	0.67	0.90	21	empty
5	358	0.66	0.80	49	empty

Interfaces

7 interfaces between chains.

A–B · 3197 Å² buried · 14 hydrogen bonds · protein-protein
E–D · 3152 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 3025 Å² buried · 21 hydrogen bonds · protein-protein
E–A · 2779 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 2691 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

6I53 · Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in complex… · the same entry in another collection · chain G against G, TM-score 1.00
P28472 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit beta-3… · a predicted model of the same protein · chain B against A, TM-score 0.99
P18507 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit gamma-2… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 0.98

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 P28472
Every structure of UniProt P14867
Every structure of UniProt P18507
Elsewhere: RCSB PDB 6I53 · PDBe 6I53 · UniProt P28472 · UniProt P14867 · UniProt P18507

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