Research workbench
Crystal structure of beta-1,4-xylosidase from bacillus subtilis, new york structural genomics consortium
Analyse Crystal structure of beta-1,4-xylosidase from bacillus subtilis, new york… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YIF
- Type
- protein
- Length
- 2,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,4-xylosidase
- EC
- 3.2.1.37
- UniProt
- P94489
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-1,4-xylosidase (EC 3.2.1.37) | protein | 532 | 1% helix, 47% strand | P94489 |
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 | 540 | 0.76 | 0.83 | 41 | empty |
| 2 | 523 | 0.76 | 0.83 | 39 | empty |
| 3 | 295 | 0.66 | 0.82 | 25 | empty |
| 4 | 316 | 0.66 | 0.81 | 25 | empty |
| 5 | 285 | 0.66 | 0.82 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2024 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2003 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 856 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 831 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1YIF · CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL… · the same entry in another collection · chain A against A, TM-score 1.00
- P94489 · AlphaFold monomer V2.0 prediction for beta-xylosidase (P94489) · 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 P94489
- Elsewhere: RCSB PDB 1YIF · PDBe 1YIF · UniProt P94489
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.