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1.75A resolution structure of 5-fluoroindole bound beta-glycosidase (W33G) from sulfolobus solfataricus
Analyse 1.75A resolution structure of 5-fluoroindole bound beta-glycosidase (W33G) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXE
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P22498
- Ligands
- 14O, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 485 | 41% helix, 17% strand | P22498 |
| B | Beta-galactosidase (EC 3.2.1.23) | protein | 488 | 41% helix, 18% strand | P22498 |
Ligands and binding sites
- 14O · 5-fluoro-1H-indole · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.74 | 0.80 | 71 | 14O, CL |
| 2 | 713 | 0.73 | 0.79 | 66 | 14O, CL |
| 3 | 64 | 0.32 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 114 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5IXE · 1.75A RESOLUTION STRUCTURE OF 5-Fluoroindole BOUND BETA-GLYCOSIDASE (W33G) FROM… · the same entry in another collection · chain A against A, TM-score 1.00
- P22498 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P22498) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22498
- Elsewhere: RCSB PDB 5IXE · PDBe 5IXE · UniProt P22498
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