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Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate
Analyse Crystal structure of human alpha-N-acetylgalactosaminidase, covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IGU
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylgalactosaminidase
- EC
- 3.2.1.49
- UniProt
- P17050
- Ligands
- 7JZ, NAG, MAN, BMA, FUC
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) | protein | 387 | 32% helix, 25% strand | P17050 |
Ligands and binding sites
- 7JZ · 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar
- GOL · Glycerol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.56 | 0.77 | 51 | GOL |
| 2 | 280 | 0.56 | 0.77 | 36 | empty |
| 3 | 99 | 0.38 | 0.76 | 16 | empty |
| 4 | 79 | 0.36 | 0.76 | 17 | empty |
| 5 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 3IGU · Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate · the same entry in another collection · chain A against A, TM-score 1.00
- P17050 · AlphaFold monomer V2.0 prediction for alpha-N-acetylgalactosaminidase (P17050) · a predicted model of the same protein · 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 P17050
- Elsewhere: RCSB PDB 3IGU · PDBe 3IGU · UniProt P17050
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