MolNFT v1 · #74320 · protein
Phosphopentomutase from bacillus cereus bound to glucose-1,6- bisphosphate
3OT9: “Phosphopentomutase from bacillus cereus bound to glucose-1,6- bisphosphate”. X-ray diffraction, 2 ligands (G16, MN), 6 pockets (best druggability 0.78). MolNFT v1 #74320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OT9
- Type
- protein
- Length
- 1,171 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopentomutase
- EC
- 5.4.2.7
- UniProt
- Q818Z9
- Ligands
- G16, MN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopentomutase (EC 5.4.2.7) | protein | 391 | 34% helix, 21% strand | Q818Z9 |
| B, C | Phosphopentomutase (EC 5.4.2.7) | protein | 390 | 36% helix, 21% strand | Q818Z9 |
Ligands and binding sites
- G16 · 1,6-di-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- MN · Manganese (II) ion · metal · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.78 | 0.80 | 94 | G16 |
| 2 | 836 | 0.74 | 0.78 | 58 | empty |
| 3 | 314 | 0.68 | 0.82 | 31 | empty |
| 4 | 486 | 0.67 | 0.79 | 60 | empty |
| 5 | 107 | 0.34 | 0.73 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–C · 889 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 348 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3OT9 · Phosphopentomutase from Bacillus cereus bound to glucose-1,6-bisphosphate · the same entry in another collection · chain A against A, 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 3OT9 · PDBe 3OT9 · UniProt Q818Z9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.