MolNFT v1 · #153351 · protein
Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl
6JBS · Beta-D-XYLOSIDASE/BETA-D-glucosidase: “Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.74). MolNFT v1 #153351 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JBS
- Type
- protein
- Length
- 3,045 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
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 762 | 27% helix, 21% strand | G8GLP2 |
| B, C, D | Beta-D-XYLOSIDASE/BETA-D-glucosidase | protein | 761 | 27% helix, 20% strand | G8GLP2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 28 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
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 | 66 | 0.74 | 0.99 | 28 | empty |
| 2 | 61 | 0.72 | 0.98 | 23 | empty |
| 3 | 797 | 0.71 | 0.77 | 69 | empty |
| 4 | 56 | 0.71 | 0.98 | 22 | empty |
| 5 | 59 | 0.71 | 0.98 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1610 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1598 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 912 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6JBS · Bifunctional xylosidase/glucosidase LXYL · 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 6JBS · PDBe 6JBS · UniProt G8GLP2
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