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Structure of a glycoside hydrolase family 3 beta-N- acetylglucosaminidase from paenibacillus sp. str. fpu-7

Analyse Structure of a glycoside hydrolase family 3 beta-N- acetylglucosaminidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K5J
Type: protein
Length: 526 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GH3 beta-N-acetylglucosaminidase
EC: 3.2.1.52
Ligands: NAG
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GH3 beta-N-acetylglucosaminidase (EC 3.2.1.52)	protein	526	42% helix, 13% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.65	0.89	29	NAG, GOL
2	135	0.47	0.78	25	empty
3	145	0.43	0.75	21	empty
4	82	0.38	0.77	18	empty
5	95	0.37	0.76	21	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

6K5J · Structure of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6K5J · PDBe 6K5J

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