Research workbench
Insights into hunter syndrome from the structure of iduronate-2- sulfatase
Analyse Insights into hunter syndrome from the structure of iduronate-2- sulfatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FQL
- Type
- protein
- Length
- 507 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iduronate-2-sulfatase
- EC
- 3.1.6.13
- UniProt
- P22304
- Ligands
- NAG, FUC, CA, CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iduronate-2-sulfatase (EC 3.1.6.13) | protein | 507 | 30% helix, 21% strand | P22304 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.58 | 0.77 | 29 | empty |
| 2 | 311 | 0.55 | 0.75 | 38 | empty |
| 3 | 102 | 0.44 | 0.78 | 19 | empty |
| 4 | 118 | 0.42 | 0.76 | 22 | CL |
Modifications
Observed in the structure: 7 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 5FQL · Insights into Hunter syndrome from the structure of iduronate-2- sulfatase · the same entry in another collection · chain A against A, TM-score 1.00
- P22304 · AlphaFold monomer V2.0 prediction for iduronate 2-sulfatase (P22304) · 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 P22304
- Elsewhere: RCSB PDB 5FQL · PDBe 5FQL · UniProt P22304
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