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The structure of hypocrea jecorina beta-xylosidase XYL3A (BXL1)
Analyse The structure of hypocrea jecorina beta-xylosidase XYL3A (BXL1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A7M
- Type
- protein
- Length
- 1,527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- Q92458
- Ligands
- NAG, MAN, BMA, ZN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 761 | 31% helix, 19% strand | Q92458 |
| B | Beta-xylosidase (EC 3.2.1.37) | protein | 766 | 30% helix, 19% strand | Q92458 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
- ZN · Zinc ion · metal · 21 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.88 | 0.89 | 138 | empty |
| 2 | 71 | 0.75 | 0.98 | 23 | empty |
| 3 | 69 | 0.74 | 0.98 | 24 | empty |
| 4 | 240 | 0.69 | 0.85 | 30 | empty |
| 5 | 94 | 0.43 | 0.79 | 21 | TRS, GOL, ACT |
Interfaces
1 interface between chains.
- A–B · 1727 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 5A7M · The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) · 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 Q92458
- Elsewhere: RCSB PDB 5A7M · PDBe 5A7M · UniProt Q92458
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