MolNFT v1 · #113397 · protein
The structure of hypocrea jecorina beta-xylosidase XYL3A (BXL1) in complex with 4-thioxylobiose
5AE6: “The structure of hypocrea jecorina beta-xylosidase XYL3A (BXL1) in complex with 4-thioxylobiose”. X-ray diffraction, 6 ligands (TXB, NAG, BMA), 8 pockets (best druggability 0.88). MolNFT v1 #113397 on GenesisL1: 3D structure…
- PDB
- 5AE6
- Type
- protein
- Length
- 1,529 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
- TXB, NAG, BMA, MAN, XYP, ZN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 762 | 31% helix, 19% strand | Q92458 |
| B | Beta-xylosidase (EC 3.2.1.37) | protein | 767 | 31% helix, 20% strand | Q92458 |
Ligands and binding sites
- TXB · 4-deoxy-4-thio-alpha-D-xylopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 12 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 | 1039 | 0.88 | 0.90 | 144 | empty |
| 2 | 69 | 0.75 | 0.99 | 20 | empty |
| 3 | 66 | 0.75 | 0.99 | 21 | empty |
| 4 | 219 | 0.71 | 0.87 | 32 | empty |
| 5 | 112 | 0.49 | 0.80 | 22 | TXB, XYP |
Interfaces
1 interface between chains.
- A–B · 1833 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 5AE6 · The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) in complex with… · 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 5AE6 · PDBe 5AE6 · UniProt Q92458
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