MolNFT v1 · #177908 · protein
Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl with intermediate substrate xylose
7EY1 · Beta-D-XYLOSIDASE/BETA-D-glucosidase: “Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl with intermediate substrate xylose”. X-ray diffraction, 6 ligands (BKR, XYZ, NAG), 20 pockets (best druggability 0.73). MolNFT v1 #177908 on GenesisL1…
- PDB
- 7EY1
- Type
- protein
- Length
- 3,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-XYLOSIDASE/BETA-D-glucosidase
- UniProt
- G8GLP2
- Ligands
- BKR, XYZ, NAG, MAN, BMA, XYP
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 756 | 28% helix, 21% strand | G8GLP2 |
Ligands and binding sites
- BKR · Deacetyltaxol · ligand · 2 copies · chains A, B
- XYZ · beta-D-xylofuranose · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 23 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- XYP · beta-D-xylopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.99 | 23 | empty |
| 2 | 66 | 0.73 | 0.98 | 24 | empty |
| 3 | 67 | 0.72 | 0.98 | 25 | empty |
| 4 | 55 | 0.71 | 0.98 | 23 | empty |
| 5 | 303 | 0.68 | 0.83 | 53 | NAG |
Interfaces
2 interfaces between chains.
- B–C · 1605 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 271 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 glycan, 12 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7EY1 · Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose · 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 G8GLP2
- Elsewhere: RCSB PDB 7EY1 · PDBe 7EY1 · UniProt G8GLP2
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