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The structure of alpha-N-acetylgalactosaminidase

Analyse The structure of alpha-N-acetylgalactosaminidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KTB
Type: protein
Length: 388 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-N-acetylgalactosaminidase
EC: 3.2.1.49
Ligands: NAG, SO4
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-N-acetylgalactosaminidase (EC 3.2.1.49)	protein	388	32% helix, 24% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A
GOL · Glycerol · additive · 12 copies · chains A
ACY · Acetic acid · additive · 2 copies · 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	59	0.39	0.80	18	GOL

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

1KTB · The Structure of alpha-N-Acetylgalactosaminidase · 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 1KTB · PDBe 1KTB

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