Research workbench
Phosphopentomutase S154G variant soaked with 2,3-dideoxyribose 5- phosphate
Analyse Phosphopentomutase S154G 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
- 4LRB
- 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
- 1X4, MN
- Pockets
- 5 · 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 | 35% helix, 21% strand | Q818Z9 |
| B, C | Phosphopentomutase (EC 5.4.2.7) | protein | 390 | 35% helix, 22% strand | Q818Z9 |
Ligands and binding sites
- 1X4 · 2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- MN · Manganese (II) ion · metal · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.78 | 0.80 | 100 | 1X4 |
| 2 | 1069 | 0.73 | 0.76 | 76 | empty |
| 3 | 509 | 0.68 | 0.79 | 46 | empty |
| 4 | 510 | 0.68 | 0.79 | 63 | empty |
| 5 | 50 | 0.24 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 898 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 4LRB · Phosphopentomutase S154G 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 A 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 Q818Z9
- Elsewhere: RCSB PDB 4LRB · PDBe 4LRB · UniProt Q818Z9
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