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X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (elic) in a desensitized state

Analyse X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SXU
Type: protein
Length: 3,080 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-aminobutyric-acid receptor subunit beta-1
UniProt: E0SJQ4
Ligands: BRJ, 3CN, CL
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Gamma-aminobutyric-acid receptor subunit beta-1	protein	308	30% helix, 33% strand	E0SJQ4

Ligands and binding sites

BRJ · 2-bromoethanol · ligand · 32 copies · chains A, B, C, D, E, F, G, H, I, J
3CN · 3-aminopropane · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
CL · Chloride ion · ion · 2 copies · chains C, I, J
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.84	0.85	118	BRJ, 3CN
2	1131	0.84	0.85	111	BRJ, 3CN
3	178	0.83	0.97	20	empty
4	860	0.83	0.85	92	BRJ, 3CN
5	842	0.83	0.85	111	BRJ, 3CN

Interfaces

19 interfaces between chains.

F–J · 2600 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 2597 Å² buried · 23 hydrogen bonds · protein-protein
F–G · 2594 Å² buried · 27 hydrogen bonds · protein-protein
A–E · 2585 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 2581 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5SXU · X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC)… · the same entry in another collection · chain A against A, TM-score 1.00

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 E0SJQ4
Elsewhere: RCSB PDB 5SXU · PDBe 5SXU · UniProt E0SJQ4

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