Research workbench
Crystal structure of GH127 beta-L-arabinofuranosidase HYPBA1 from bifidobacterium longum arabinose complex form
Analyse Crystal structure of GH127 beta-L-arabinofuranosidase HYPBA1 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WKX
- Type
- protein
- Length
- 657 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
- FUB, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-reducing end beta-L-arabinofuranosidase (EC 3.2.1.185) | protein | 657 | 40% helix, 18% strand | E8MGH8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.70 | 0.82 | 68 | FUB |
| 2 | 384 | 0.67 | 0.80 | 36 | empty |
| 3 | 295 | 0.58 | 0.77 | 33 | empty |
| 4 | 54 | 0.35 | 0.78 | 21 | empty |
Compared structures
- 3WKX · Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum… · 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 3WKX · PDBe 3WKX · UniProt E8MGH8
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