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Trypanosoma rangeli sialidase in complex with 2,3- difluorosialic acid (covalent intermediate)

Analyse Trypanosoma rangeli sialidase in complex with 2,3- difluorosialic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FHR
Type: protein
Length: 625 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialidase
EC: 3.2.1.18
Ligands: FSI, SO4
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialidase (EC 3.2.1.18)	protein	625	7% helix, 47% strand	—

Ligands and binding sites

FSI · 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	254	0.57	0.78	24	empty
2	238	0.57	0.78	30	FSI
3	172	0.48	0.76	35	SO4
4	65	0.30	0.74	19	empty

Modifications

Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

2FHR · Trypanosoma Rangeli Sialidase In Complex With 2,3- Difluorosialic Acid (Covalent… · 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
Elsewhere: RCSB PDB 2FHR · PDBe 2FHR

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