MolNFT v1 · #36324 · protein

Crystal structure of the human sialidase NEU2 E111Q mutant in complex with dana inhibitor

2F25 · Sialidase 2: “Crystal structure of the human sialidase NEU2 E111Q mutant in complex with dana inhibitor”. X-ray diffraction, 1 ligand (DAN), 7 pockets (best druggability 0.71). MolNFT v1 #36324 on GenesisL1: 3D structure, binding…

PDB: 2F25
Type: protein
Length: 743 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialidase 2
EC: 3.2.1.18
UniProt: Q9Y3R4
Ligands: DAN
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialidase 2 (EC 3.2.1.18)	protein	373	8% helix, 51% strand	Q9Y3R4
B	Sialidase 2 (EC 3.2.1.18)	protein	370	8% helix, 50% strand	Q9Y3R4

Ligands and binding sites

DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.71	0.88	39	empty
2	349	0.64	0.79	29	empty
3	188	0.63	0.84	31	DAN
4	307	0.63	0.80	26	empty
5	209	0.63	0.83	33	DAN, EPE

Interfaces

1 interface between chains.

A–B · 1038 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2F25 · Crystal Structure of the Human Sialidase Neu2 E111Q Mutant in Complex with DANA Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y3R4 · AlphaFold monomer V2.0 prediction for sialidase-2 (Q9Y3R4) · 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 Q9Y3R4
Elsewhere: RCSB PDB 2F25 · PDBe 2F25 · UniProt Q9Y3R4

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