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The structure of clostridium perfringens nani sialidase and its catalytic intermediates

Analyse The structure of clostridium perfringens nani sialidase and its catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VK6
Type: protein
Length: 448 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exo-alpha-sialidase
EC: 3.2.1.18
UniProt: Q59310
Ligands: DAN, MG, CA
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exo-alpha-sialidase (EC 3.2.1.18)	protein	448	2% helix, 48% strand	Q59310

Ligands and binding sites

DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
MG · Magnesium ion · metal · 4 copies · chains A
CA · Calcium ion · metal · chains A
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.64	0.81	36	empty
2	237	0.62	0.81	31	empty
3	126	0.52	0.81	22	DAN
4	65	0.32	0.76	17	empty

Compared structures

2VK6 · The structure of clostridium perfringens nani sialidase and its catalytic intermediates · the same entry in another collection · 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 Q59310
Elsewhere: RCSB PDB 2VK6 · PDBe 2VK6 · UniProt Q59310

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