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The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from clostridium perfringens

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PDB: 5FR0
Type: protein
Length: 576 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-N-acetylgalactosaminidase
UniProt: A0A0H2YNR7
Ligands: SIZ, PO4
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-N-acetylgalactosaminidase	protein	576	31% helix, 28% strand	A0A0H2YNR7

Ligands and binding sites

SIZ · 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-galactopyranose · ligand · chains A
PO4 · Phosphate ion · ion · chains A

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

Pockets

6 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	444	0.65	0.78	52	empty
2	98	0.56	0.85	21	SIZ
3	180	0.51	0.77	29	empty
4	92	0.40	0.77	20	empty
5	79	0.37	0.77	22	empty

Compared structures

5FR0 · The details of glycolipid glycan hydrolysis by the structural analysis of a family 123… · 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 A0A0H2YNR7
Elsewhere: RCSB PDB 5FR0 · PDBe 5FR0 · UniProt A0A0H2YNR7

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