Research workbench
Structure of the alpha-L-arabinofuranosidase ARB93A from fusarium graminearum in complexe with an iminosugar inhibitor
Analyse Structure of the alpha-L-arabinofuranosidase ARB93A from fusarium graminearum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDT
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-1,5-alpha-L-arabinofuranobiosidase
- EC
- 3.2.1.55
- UniProt
- B8ZY56
- Ligands
- EDG, AHR, MN, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-1,5-alpha-L-arabinofuranobiosidase (EC 3.2.1.55) | protein | 359 | 1% helix, 45% strand | B8ZY56 |
Ligands and binding sites
- EDG · 1,4-dideoxy-1,4-imino-L-arabinitol · ligand · chains A
- AHR · alpha-L-arabinofuranose · sugar · chains A
- MN · Manganese (II) ion · metal · 5 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.71 | 0.81 | 29 | SO4, MN |
| 2 | 220 | 0.54 | 0.77 | 34 | EDG, AHR, ACT |
| 3 | 73 | 0.34 | 0.76 | 15 | empty |
Compared structures
- 2YDT · STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A from FUSARIUM Graminearum in complexe… · 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 B8ZY56
- Elsewhere: RCSB PDB 2YDT · PDBe 2YDT · UniProt B8ZY56
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.