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Crystal structure of apo nanb sialidase from streptococcus pneumoniae at pH 8.0 with mpd as the cryoprotectant

Analyse Crystal structure of apo nanb sialidase from streptococcus pneumoniae at pH 8.0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XIO
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

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	303	0.62	0.80	35	empty
2	224	0.54	0.78	34	empty
3	229	0.52	0.76	39	empty
4	243	0.52	0.76	30	empty
5	57	0.33	0.77	14	empty

Compared structures

4XIO · Crystal structure of apo NanB sialidase from streptococcus pneumoniae at pH 8.0 with MPD… · 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 4XIO · PDBe 4XIO · UniProt Q54727

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