Research workbench
Crystal structure of human alpha-L-iduronidase complex with alpha-L- iduronic acid
Analyse Crystal structure of human alpha-L-iduronidase complex with alpha-L- iduronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OBR
- Type
- protein
- Length
- 1,201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-iduronidase
- EC
- 3.2.1.76
- UniProt
- P35475
- Ligands
- IDR, NAG, MAN, BMA, CL, SO4
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 595 | 26% helix, 31% strand | P35475 |
| B | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 606 | 25% helix, 30% strand | P35475 |
Ligands and binding sites
- IDR · alpha-L-idopyranuronic acid · 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 · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.62 | 0.78 | 49 | NAG, GOL |
| 2 | 146 | 0.56 | 0.82 | 20 | empty |
| 3 | 134 | 0.54 | 0.81 | 21 | empty |
| 4 | 136 | 0.48 | 0.79 | 36 | empty |
| 5 | 168 | 0.47 | 0.76 | 25 | TLA |
Interfaces
1 interface between chains.
- A–B · 282 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 4OBR · Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P35475 · AlphaFold monomer V2.0 prediction for alpha-L-iduronidase (P35475) · 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 P35475
- Elsewhere: RCSB PDB 4OBR · PDBe 4OBR · UniProt P35475
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.