Research workbench
Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5- phosphate
Analyse Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5- phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LR9
- Type
- protein
- Length
- 1,172 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
- 1X4, MN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphopentomutase (EC 5.4.2.7) | protein | 391 | 35% helix, 21% strand | Q818Z9 |
| C | Phosphopentomutase (EC 5.4.2.7) | protein | 390 | 34% helix, 21% strand | Q818Z9 |
Ligands and binding sites
- 1X4 · 2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.77 | 0.80 | 88 | 1X4 |
| 2 | 1192 | 0.76 | 0.79 | 99 | empty |
| 3 | 428 | 0.67 | 0.80 | 44 | empty |
| 4 | 57 | 0.41 | 0.82 | 16 | empty |
| 5 | 56 | 0.36 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 912 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 319 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 4LR9 · Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5-phosphate · 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 C 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 4LR9 · PDBe 4LR9 · UniProt Q818Z9
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