Research workbench
Phosphopentomutase S154G variant soaked with ribose 5-phosphate
Analyse Phosphopentomutase S154G variant soaked with ribose 5-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LRF
- 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
- HSX, MN
- Pockets
- 6 · best druggability 0.77
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, 21% strand | Q818Z9 |
Ligands and binding sites
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 12 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.77 | 0.80 | 86 | HSX |
| 2 | 1080 | 0.73 | 0.76 | 73 | empty |
| 3 | 497 | 0.70 | 0.80 | 45 | empty |
| 4 | 516 | 0.68 | 0.78 | 61 | empty |
| 5 | 51 | 0.36 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 902 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 324 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 covalent (phosphorylation, covalent ligand).
Compared structures
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 4LRF · PDBe 4LRF · UniProt Q818Z9
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