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Ruminococcus gnavus it-sialidase CBM40 bound to ALPHA2,6 sialyllactose

Analyse Ruminococcus gnavus it-sialidase CBM40 bound to ALPHA2,6 sialyllactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ER4
Type: protein
Length: 383 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BNR/ASP-box repeat protein
UniProt: A7B557
Ligands: BGC, GAL, SIA
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BNR/ASP-box repeat protein	protein	194	8% helix, 48% strand	A7B557
B	BNR/ASP-box repeat protein	protein	189	7% helix, 47% strand	A7B557

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
GAL · beta-D-galactopyranose · sugar · 2 copies
SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B
1PE · Pentaethylene glycol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	232	0.59	0.80	48	SIA, GOL

Interfaces

1 interface between chains.

A–B · 757 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6ER4 · Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose · 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 A7B557
Elsewhere: RCSB PDB 6ER4 · PDBe 6ER4 · UniProt A7B557

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