MolNFT v1 · #109973 · protein

Crystal structure of nanb sialidase from streptococcus pneumoniae in complex with dmso

4XIK · Sialidase B: “Crystal structure of nanb sialidase from streptococcus pneumoniae in complex with dmso”. X-ray diffraction, 6 pockets (best druggability 0.62). MolNFT v1 #109973 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4XIK
Type: protein
Length: 658 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
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialidase B (EC 3.2.1.18)	protein	658	3% helix, 45% strand	Q54727

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · 5 copies · chains A

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

Pockets

6 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	263	0.62	0.81	25	DMS
2	298	0.61	0.79	38	DMS
3	260	0.54	0.76	33	empty
4	242	0.53	0.76	44	DMS
5	62	0.39	0.79	16	empty

Compared structures

4XIK · Crystal structure of NanB sialidase from streptococcus pneumoniae in complex with DMSO · 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 4XIK · PDBe 4XIK · UniProt Q54727

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