Research workbench
Bacillus cereus phosphopentomutase T85E variant soaked with glucose 1, 6-bisphosphate
Analyse Bacillus cereus phosphopentomutase T85E variant soaked with glucose 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UNY
- Type
- protein
- Length
- 2,343 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopentomutase
- EC
- 5.4.2.7
- UniProt
- Q818Z9
- Ligands
- MN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Phosphopentomutase (EC 5.4.2.7) | protein | 391 | 35% helix, 21% strand | Q818Z9 |
| B, C, D | Phosphopentomutase (EC 5.4.2.7) | protein | 390 | 35% helix, 21% strand | Q818Z9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 16 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.76 | 0.79 | 82 | empty |
| 2 | 808 | 0.74 | 0.79 | 62 | empty |
| 3 | 531 | 0.68 | 0.78 | 50 | empty |
| 4 | 529 | 0.68 | 0.78 | 44 | empty |
| 5 | 794 | 0.67 | 0.75 | 82 | empty |
Interfaces
6 interfaces between chains.
- D–E · 908 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 604 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 137 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 43 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3UNY · Bacillus cereus phosphopentomutase T85E variant soaked with glucose 1,6-bisphosphate · the same entry in another collection · chain F against F, TM-score 1.00
- Q818Z9 · AlphaFold monomer V2.0 prediction for phosphopentomutase (Q818Z9) · 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 Q818Z9
- Elsewhere: RCSB PDB 3UNY · PDBe 3UNY · UniProt Q818Z9
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