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Crystal structure of human alpha-L-iduronidase complex with 2-deoxy-2- fluoro-alpha-L-idopyranosyluronic acid fluoride
Analyse Crystal structure of human alpha-L-iduronidase complex with 2-deoxy-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KH2
- Type
- protein
- Length
- 1,202 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
- FIF, SRT, NAG, MAN, BMA, CL
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 595 | 26% helix, 30% strand | P35475 |
| B | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 607 | 26% helix, 31% strand | P35475 |
Ligands and binding sites
- FIF · 2,6-anhydro-5-deoxy-5-fluoro-L-idonic acid · ligand · 2 copies · chains A, B
- SRT · S,R meso-tartaric acid · ligand · chains 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
- GOL · Glycerol · additive · 6 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.69 | 0.96 | 20 | empty |
| 2 | 663 | 0.68 | 0.76 | 79 | NAG, GOL |
| 3 | 50 | 0.66 | 0.96 | 17 | GOL |
| 4 | 166 | 0.56 | 0.81 | 23 | empty |
| 5 | 161 | 0.56 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 299 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 covalent (N-glycosylation, covalent ligand).
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 P35475
- Elsewhere: RCSB PDB 4KH2 · PDBe 4KH2 · UniProt P35475
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