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The three-dimensional structure of beta-fructosidase (invertase) from thermotoga maritima
Analyse The three-dimensional structure of beta-fructosidase (invertase) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UYP
- Type
- protein
- Length
- 2,592 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-fructosidase
- EC
- 3.2.1.26
- UniProt
- O33833
- Ligands
- NA, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-fructosidase (EC 3.2.1.26) | protein | 432 | 3% helix, 59% strand | O33833 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 14 copies · chains A, D, B, C, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.76 | 0.79 | 89 | SO4 |
| 2 | 486 | 0.71 | 0.81 | 52 | empty |
| 3 | 633 | 0.71 | 0.78 | 59 | empty |
| 4 | 599 | 0.68 | 0.77 | 47 | SO4 |
| 5 | 435 | 0.68 | 0.80 | 58 | SO4 |
Interfaces
8 interfaces between chains.
- D–E · 1261 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 610 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 576 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 464 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1UYP · The three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima · the same entry in another collection · chain F against F, TM-score 1.00
- O33833 · AlphaFold monomer V2.0 prediction for beta-fructosidase (O33833) · a predicted model of the same protein · chain F 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 O33833
- Elsewhere: RCSB PDB 1UYP · PDBe 1UYP · UniProt O33833
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