MolNFT v1 · #24019 · protein
Crystal structure of beta-D-xylosidase from thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase
1UHV · Beta-xylosidase: “Crystal structure of beta-D-xylosidase from thermoanaerobacterium saccharolyticum, a family 39 glycoside…”. X-ray diffraction, 1 ligand (DFX), 20 pockets (best druggability 0.76). MolNFT v1 #24019 on GenesisL1: 3D…
- PDB
- 1UHV
- Type
- protein
- Length
- 2,000 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- P36906
- Ligands
- DFX
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-xylosidase (EC 3.2.1.37) | protein | 500 | 31% helix, 26% strand | P36906 |
Ligands and binding sites
- DFX · 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol · ligand · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.76 | 0.81 | 81 | DFX |
| 2 | 79 | 0.73 | 0.97 | 30 | empty |
| 3 | 537 | 0.73 | 0.82 | 40 | empty |
| 4 | 78 | 0.73 | 0.97 | 30 | empty |
| 5 | 70 | 0.72 | 0.97 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2745 Ų buried · 58 hydrogen bonds · protein-protein
- B–D · 2704 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 1648 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1647 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1UHV · 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 1UHV · PDBe 1UHV · UniProt P36906
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