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Lysenin sphingomyelin complex

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

PDB: 3ZXG
Type: protein
Length: 586 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysenin
UniProt: O18423
Ligands: 0SM, SO4
Pockets: 2 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysenin	protein	293	2% helix, 53% strand	O18423
B	Lysenin	protein	293	2% helix, 50% strand	O18423

Ligands and binding sites

0SM · Trimethyl-[2-[[(2S,3S)-2-(octadecanoylamino)-3-oxidanyl-butoxy]-oxidanyl-phosphoryl]oxyethyl]azanium · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

2 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	63	0.33	0.76	19	empty
2	71	0.32	0.75	15	empty

Compared structures

3ZXG · lysenin sphingomyelin complex · the same entry in another collection · chain A against A, TM-score 1.00
O18423 · AlphaFold monomer V2.0 prediction for lysenin (O18423) · a predicted model of the same protein · chain A against A, TM-score 0.59

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 O18423
Elsewhere: RCSB PDB 3ZXG · PDBe 3ZXG · UniProt O18423

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