MolNFT v1 · #176312 · protein
GH127 beta-L-arabinofuranosidase HYPBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-ångström resolution
7DIF · Non-reducing end beta-L-arabinofuranosidase: “GH127 beta-L-arabinofuranosidase HYPBA1 covalently complexed with beta-L-arabinofuranose-configured…”. X-ray diffraction, 3 ligands (FE0, ZN, K), 3 pockets (best druggability 0.70).…
- PDB
- 7DIF
- Type
- protein
- Length
- 656 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-reducing end beta-L-arabinofuranosidase
- EC
- 3.2.1.185
- UniProt
- E8MGH8
- Ligands
- FE0, ZN, K
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-reducing end beta-L-arabinofuranosidase (EC 3.2.1.185) | protein | 656 | 39% helix, 17% strand | E8MGH8 |
Ligands and binding sites
- FE0 · (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- K · Potassium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.70 | 0.83 | 44 | FE0 |
| 2 | 372 | 0.66 | 0.80 | 39 | empty |
| 3 | 321 | 0.60 | 0.77 | 34 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DIF · GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- E8MGH8 · AlphaFold monomer V2.0 prediction for non-reducing end beta-L- arabinofuranosidase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 E8MGH8
- Elsewhere: RCSB PDB 7DIF · PDBe 7DIF · UniProt E8MGH8
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