Research workbench
The bacterial orthologue of human a-L-iduronidase does not need N- glycan post-translational modifications to be catalytically competent: crystallography and QM/MM insights into mucopolysaccharidosis I
Analyse The bacterial orthologue of human a-L-iduronidase does not need N- glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NDX
- Type
- protein
- Length
- 606 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase
- UniProt
- A0A1B8R7L2
- Ligands
- 8U8, SO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase | protein | 606 | 27% helix, 29% strand | A0A1B8R7L2 |
Ligands and binding sites
- 8U8 · (2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl) oxane-2-carboxylic acid · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.63 | 0.84 | 39 | SO4 |
| 2 | 209 | 0.52 | 0.77 | 36 | 8U8 |
| 3 | 71 | 0.48 | 0.84 | 20 | empty |
| 4 | 127 | 0.46 | 0.77 | 22 | 8U8 |
| 5 | 64 | 0.42 | 0.81 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NDX · The bacterial orthologue of Human a-L-iduronidase does not need N-glycan… · 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
- Every structure of UniProt A0A1B8R7L2
- Elsewhere: RCSB PDB 5NDX · PDBe 5NDX · UniProt A0A1B8R7L2
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