MolNFT v1 · #110504 · protein

Nanb plus optactamide

4XYX · Sialidase B: “Nanb plus optactamide”. X-ray diffraction, 2 ligands (43Z, PO4), 5 pockets (best druggability 0.61). MolNFT v1 #110504 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XYX
Type: protein
Length: 660 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialidase B
EC: 3.2.1.18
UniProt: Q54727
Ligands: 43Z, PO4
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialidase B (EC 3.2.1.18)	protein	660	3% helix, 44% strand	Q54727

Ligands and binding sites

43Z · Optactamide · ligand · chains A
PO4 · Phosphate ion · ion · 18 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	337	0.61	0.78	28	43Z
2	302	0.60	0.78	39	PO4
3	243	0.53	0.76	31	PO4
4	208	0.52	0.77	32	PO4
5	93	0.45	0.79	18	PO4

Compared structures

4XYX · NanB plus Optactamide · the same entry in another collection · chain A against A, TM-score 1.00
Q54727 · AlphaFold monomer V2.0 prediction for sialidase B (Q54727) · a predicted model of the same protein · 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 Q54727
Elsewhere: RCSB PDB 4XYX · PDBe 4XYX · UniProt Q54727

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