MolNFT v1 · #177909 · protein
Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl D300N mutant with intermediate substrate xylose
7EY2 · Beta-D-XYLOSIDASE/BETA-D-glucosidase: “Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl D300N mutant with intermediate substrate xylose”. X-ray diffraction, 5 ligands (XYL, XYZ, NAG), 20 pockets (best druggability 0.77). MolNFT v1 #177909…
- PDB
- 7EY2
- Type
- protein
- Length
- 4,542 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-XYLOSIDASE/BETA-D-glucosidase
- UniProt
- G8GLP2
- Ligands
- XYL, XYZ, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 758 | 27% helix, 21% strand | G8GLP2 |
| B | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 758 | 27% helix, 21% strand | G8GLP2 |
| C, D | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 756 | 27% helix, 21% strand | G8GLP2 |
| E, F | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 757 | 27% helix, 21% strand | G8GLP2 |
Ligands and binding sites
- XYL · Xylitol · ligand · 3 copies · chains C, D, E
- XYZ · beta-D-xylofuranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 41 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 19 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.77 | 0.79 | 104 | NAG |
| 2 | 1043 | 0.76 | 0.79 | 99 | NAG |
| 3 | 67 | 0.73 | 0.98 | 23 | empty |
| 4 | 73 | 0.73 | 0.98 | 29 | empty |
| 5 | 63 | 0.73 | 0.98 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1598 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 857 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 299 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EY2 · Bifunctional xylosidase/glucosidase LXYL D300N mutant 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 7EY2 · PDBe 7EY2 · UniProt G8GLP2
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