Research workbench

A receptor molecule

Analyse A receptor molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BUO
Type: protein
Length: 197 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid beta A4 protein
UniProt: P05067
Ligands: SGN, IDS, ZN, CA, MG, SCN, SO4
Pockets: 1 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amyloid beta A4 protein	protein	185	90% helix, 0% strand	P05067
B	Amyloid beta A4 protein	protein	12	33% helix, 0% strand	P05067

Ligands and binding sites

SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar
ZN · Zinc ion · metal · 6 copies · chains A
CA · Calcium ion · metal
MG · Magnesium ion · metal · chains A
SCN · Thiocyanate ion · ion · 3 copies · chains A
SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 3 copies · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.40	0.75	17	ZN, SCN

Interfaces

1 interface between chains.

A–B · 233 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5BUO · A receptor molecule · the same entry in another collection · chain A against A, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · 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 P05067
Elsewhere: RCSB PDB 5BUO · PDBe 5BUO · UniProt P05067

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