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Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) catalytic domain auto-inhibited by pro- peptide

Analyse Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PKH
Type: protein
Length: 307 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase
UniProt: F1QSF9
Ligands: NAG, BMA, MAN, FUC
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase	protein	307	19% helix, 35% strand	F1QSF9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.43	0.81	17	empty

Modifications

Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6PKH · Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)… · 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 F1QSF9
Elsewhere: RCSB PDB 6PKH · PDBe 6PKH · UniProt F1QSF9

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