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The structure and function of an arabinan-specific alpha-1,2- arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases
Analyse The structure and function of an arabinan-specific alpha-1,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QEF
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-XYLOSIDASE/ALPHA-L-arabinfuranosidase, GLY43N
- EC
- 3.2.1.-
- UniProt
- B3PD60
- Ligands
- AHR, CA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-XYLOSIDASE/ALPHA-L-arabinfuranosidase, GLY43N (EC 3.2.1.-) | protein | 296 | 2% helix, 49% strand | B3PD60 |
| B | Beta-XYLOSIDASE/ALPHA-L-arabinfuranosidase, GLY43N (EC 3.2.1.-) | protein | 297 | 2% helix, 49% strand | B3PD60 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.74 | 0.88 | 52 | empty |
| 2 | 419 | 0.72 | 0.83 | 69 | AHR, EDO |
| 3 | 269 | 0.54 | 0.76 | 22 | empty |
| 4 | 259 | 0.54 | 0.76 | 22 | empty |
| 5 | 52 | 0.31 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3QEF · The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase… · 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 B3PD60
- Elsewhere: RCSB PDB 3QEF · PDBe 3QEF · UniProt B3PD60
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