MolNFT v1 · #18696 · protein
Crystal structure of beta-D-xylosidase from thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase
1PX8 · Beta-xylosidase: “Crystal structure of beta-D-xylosidase from thermoanaerobacterium saccharolyticum, a family 39 glycoside…”. X-ray diffraction, 1 ligand (XYP), 10 pockets (best druggability 0.75). MolNFT v1 #18696 on GenesisL1: 3D…
- PDB
- 1PX8
- Type
- protein
- Length
- 1,000 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- P36906
- Ligands
- XYP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylosidase (EC 3.2.1.37) | protein | 500 | 33% helix, 25% strand | P36906 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.75 | 0.83 | 43 | empty |
| 2 | 230 | 0.66 | 0.84 | 27 | empty |
| 3 | 235 | 0.65 | 0.83 | 30 | empty |
| 4 | 106 | 0.54 | 0.83 | 28 | empty |
| 5 | 93 | 0.53 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1646 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1PX8 · Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a… · the same entry in another collection · chain A against A, TM-score 1.00
- P36906 · AlphaFold monomer V2.0 prediction for beta-xylosidase (P36906) · a predicted model of the same protein · 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 P36906
- Elsewhere: RCSB PDB 1PX8 · PDBe 1PX8 · UniProt P36906
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