MolNFT v1 · #68781 · protein

X-ray crystal structure of the E2 domain of apl-1 from C. elegans, in complex with sucrose octasulfate (sos)

3K6B · Beta-amyloid-like protein: “X-ray crystal structure of the E2 domain of apl-1 from C. elegans, in complex with sucrose octasulfate (sos)”. X-ray diffraction, 1 ligand (GU4), 3 pockets (best druggability 0.42). MolNFT v1 #68781 on…

PDB: 3K6B
Type: protein
Length: 217 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-amyloid-like protein
UniProt: Q10651
Ligands: GU4
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-amyloid-like protein	protein	217	85% helix, 0% strand	Q10651

Ligands and binding sites

GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.42	0.77	17	empty
2	123	0.40	0.75	19	empty
3	68	0.28	0.73	18	empty

Compared structures

3K6B · X-ray crystal structure of the E2 domain of APL-1 from C. elegans, in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Q10651 · AlphaFold monomer V2.0 prediction for amyloid-beta-like protein (Q10651) · a predicted model of the same protein · chain A 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 Q10651
Elsewhere: RCSB PDB 3K6B · PDBe 3K6B · UniProt Q10651

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