MolNFT v1 · #171254 · protein
Crystal structure of beta-D-xylosidase from dictyoglomus thermophilum bound to beta-D-xylopyranose
6YYI · Beta-xylosidase: “Crystal structure of beta-D-xylosidase from dictyoglomus thermophilum bound to beta-D-xylopyranose”. X-ray diffraction, 3 ligands (XYP, NA, SO4), 10 pockets (best druggability 0.71). MolNFT v1 #171254 on GenesisL1…
- PDB
- 6YYI
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- B5YB78
- Ligands
- XYP, NA, SO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylosidase (EC 3.2.1.37) | protein | 502 | 33% helix, 26% strand | B5YB78 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.71 | 0.80 | 49 | EDO |
| 2 | 234 | 0.60 | 0.80 | 35 | empty |
| 3 | 321 | 0.59 | 0.77 | 51 | EDO, CIT |
| 4 | 214 | 0.59 | 0.80 | 30 | empty |
| 5 | 212 | 0.52 | 0.76 | 32 | XYP |
Interfaces
1 interface between chains.
- A–B · 1609 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6YYI · Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to… · 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 B5YB78
- Elsewhere: RCSB PDB 6YYI · PDBe 6YYI · UniProt B5YB78
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