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Crystal structure of N-acetylgalactosaminidase in complex with galnac

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

PDB: 2IXB
Type: protein
Length: 426 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: NAD, A2G
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-N-acetylgalactosaminidase (EC 3.2.1.49)	protein	426	38% helix, 18% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

2 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	467	0.70	0.80	47	NAD, A2G
2	73	0.35	0.76	19	MPD

Compared structures

2IXB · Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC · 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 2IXB · PDBe 2IXB

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