Research workbench
Crystal structure of beta-xylosidase from bacillus pumilus
Analyse Crystal structure of beta-xylosidase from bacillus pumilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZQJ
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- P07129
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 535 | 1% helix, 46% strand | P07129 |
| B | Beta-xylosidase (EC 3.2.1.37) | protein | 533 | 1% helix, 47% strand | P07129 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.79 | 0.86 | 42 | empty |
| 2 | 284 | 0.64 | 0.81 | 26 | empty |
| 3 | 295 | 0.64 | 0.81 | 25 | empty |
| 4 | 284 | 0.59 | 0.78 | 25 | empty |
| 5 | 146 | 0.57 | 0.82 | 30 | GOL |
Interfaces
1 interface between chains.
- A–B · 2058 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
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 P07129
- Elsewhere: RCSB PDB 5ZQJ · PDBe 5ZQJ · UniProt P07129
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