MolNFT v1 · #91446 · protein
The molecular basis of mucopolysaccharidosis IV a, complex with galnac
4FDJ · N-acetylgalactosamine-6-sulfatase: “The molecular basis of mucopolysaccharidosis IV a, complex with galnac”. X-ray diffraction, 3 ligands (NAG, NGA, CA), 13 pockets (best druggability 0.74). MolNFT v1 #91446 on GenesisL1: 3D…
- PDB
- 4FDJ
- Type
- protein
- Length
- 985 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylgalactosamine-6-sulfatase
- EC
- 3.1.6.4
- UniProt
- P34059
- Ligands
- NAG, NGA, CA
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylgalactosamine-6-sulfatase (EC 3.1.6.4) | protein | 493 | 26% helix, 17% strand | P34059 |
| B | N-acetylgalactosamine-6-sulfatase (EC 3.1.6.4) | protein | 492 | 26% helix, 17% strand | P34059 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.74 | 0.98 | 22 | empty |
| 2 | 79 | 0.72 | 0.96 | 24 | empty |
| 3 | 408 | 0.63 | 0.77 | 53 | NGA |
| 4 | 403 | 0.62 | 0.77 | 53 | NGA |
| 5 | 311 | 0.56 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 4FDJ · The molecular basis of mucopolysaccharidosis IV A, complex with GalNAc · the same entry in another collection · chain A against A, TM-score 1.00
- P34059 · AlphaFold monomer V2.0 prediction for N-acetylgalactosamine-6-sulfatase (P34059) · a predicted model of the same protein · chain B 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 P34059
- Elsewhere: RCSB PDB 4FDJ · PDBe 4FDJ · UniProt P34059
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