MolNFT v1 · #57845 · protein
Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido
3AKI · Putative secreted alpha L-arabinofuranosidase II: “Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido”. X-ray diffraction, 3 ligands (AH8, NA, CL), 4 pockets (best druggability…
- PDB
- 3AKI
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted alpha L-arabinofuranosidase II
- EC
- 3.2.1.55
- UniProt
- Q82P90
- Ligands
- AH8, NA, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted alpha L-arabinofuranosidase II (EC 3.2.1.55) | protein | 448 | 7% helix, 49% strand | Q82P90 |
Ligands and binding sites
- AH8 · (2R,3R,4R,5S)-2-azido-5-(hydroxymethyl)oxolane-3,4-diol · ligand · 4 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 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 | 238 | 0.69 | 0.85 | 28 | AH8, GOL |
| 2 | 257 | 0.56 | 0.77 | 24 | empty |
| 3 | 130 | 0.38 | 0.74 | 22 | empty |
| 4 | 109 | 0.38 | 0.75 | 23 | empty |
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 Q82P90
- Elsewhere: RCSB PDB 3AKI · PDBe 3AKI · UniProt Q82P90
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