MolNFT v1 · #142032 · protein
Crystal structure of beta-xylosidase mutant (E186Q) from bacillus pumilus
5ZQX: “Crystal structure of beta-xylosidase mutant (E186Q) from bacillus pumilus”. X-ray diffraction, 1 ligand (XYP), 20 pockets (best druggability 0.78). MolNFT v1 #142032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZQX
- Type
- protein
- Length
- 2,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- P07129
- Ligands
- XYP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 536 | 1% helix, 46% strand | P07129 |
| B, D | Beta-xylosidase (EC 3.2.1.37) | protein | 533 | 1% helix, 47% strand | P07129 |
| C | Beta-xylosidase (EC 3.2.1.37) | protein | 535 | 1% helix, 47% strand | P07129 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 8 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 | 452 | 0.78 | 0.86 | 42 | empty |
| 2 | 480 | 0.77 | 0.85 | 42 | empty |
| 3 | 579 | 0.69 | 0.78 | 58 | XYP |
| 4 | 545 | 0.68 | 0.78 | 58 | XYP |
| 5 | 318 | 0.65 | 0.80 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2014 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1999 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 934 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 924 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ZQX · Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus · the same entry in another collection · chain C against C, TM-score 1.00
- P07129 · AlphaFold monomer V2.0 prediction for beta-xylosidase (P07129) · a predicted model of the same protein · chain B 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 P07129
- Elsewhere: RCSB PDB 5ZQX · PDBe 5ZQX · UniProt P07129
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