MolNFT v1 · #21550 · protein

Staphylococcal enterotoxin B complexed with GM3 trisaccharide

1SE3: “Staphylococcal enterotoxin B complexed with GM3 trisaccharide”. X-ray diffraction, 3 ligands (BGC, GAL, SIA), 1 pocket (best druggability 0.29). MolNFT v1 #21550 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SE3
Type: protein
Length: 239 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Staphylococcal enterotoxin B
UniProt: P01552
Ligands: BGC, GAL, SIA
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Staphylococcal enterotoxin B	protein	239	16% helix, 35% strand	P01552

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar
GAL · beta-D-galactopyranose · sugar · chains A
SIA · N-acetyl-alpha-neuraminic acid · sugar · 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	52	0.29	0.76	14	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1SE3 · Staphylococcal enterotoxin B complexed with GM3 trisaccharide · the same entry in another collection · chain A against A, TM-score 1.00
P01552 · AlphaFold monomer V2.0 prediction for enterotoxin type B (P01552) · 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 P01552
Elsewhere: RCSB PDB 1SE3 · PDBe 1SE3 · UniProt P01552

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