Research workbench

SIALIDASE26 co-crystallized with dana-gc

Analyse SIALIDASE26 co-crystallized with dana-gc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYV
Type: protein
Length: 2,092 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SIALIDASE26
Ligands: GC9
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	SIALIDASE26	protein	522	6% helix, 46% strand	—
C	SIALIDASE26	protein	526	6% helix, 46% strand	—

Ligands and binding sites

GC9 · 2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.71	0.79	56	GC9
2	322	0.69	0.83	27	empty
3	598	0.66	0.76	58	empty
4	345	0.66	0.81	29	empty
5	307	0.64	0.80	26	empty

Interfaces

5 interfaces between chains.

B–C · 1625 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 425 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 276 Å² buried · 1 hydrogen bond · protein-protein
A–C · 193 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 33 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MYV · Sialidase26 co-crystallized with DANA-Gc · 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 6MYV · PDBe 6MYV

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