MolNFT v1 · #91445 · protein
The molecular basis of mucopolysaccharidosis IV a
4FDI · N-acetylgalactosamine-6-sulfatase: “The molecular basis of mucopolysaccharidosis IV a”. X-ray diffraction, 2 ligands (NAG, CA), 13 pockets (best druggability 0.77). MolNFT v1 #91445 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4FDI
- Type
- protein
- Length
- 986 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, CA
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylgalactosamine-6-sulfatase (EC 3.1.6.4) | protein | 494 | 27% helix, 17% strand | P34059 |
| B | N-acetylgalactosamine-6-sulfatase (EC 3.1.6.4) | protein | 492 | 27% helix, 17% strand | P34059 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 115 | 0.77 | 0.96 | 37 | empty |
| 2 | 74 | 0.72 | 0.96 | 23 | empty |
| 3 | 448 | 0.64 | 0.77 | 52 | CIT |
| 4 | 390 | 0.62 | 0.77 | 54 | CIT |
| 5 | 306 | 0.56 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1486 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
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 4FDI · PDBe 4FDI · UniProt P34059
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