Research workbench
Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans
Analyse Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N7T
- Type
- protein
- Length
- 803 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopentomutase
- EC
- 5.4.2.7
- UniProt
- Q8DTU0
- Ligands
- MN, SO4, AZI
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopentomutase (EC 5.4.2.7) | protein | 402 | 35% helix, 21% strand | Q8DTU0 |
| B | Phosphopentomutase (EC 5.4.2.7) | protein | 401 | 34% helix, 20% strand | Q8DTU0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.78 | 0.82 | 77 | GOL |
| 2 | 367 | 0.60 | 0.77 | 39 | empty |
| 3 | 345 | 0.59 | 0.77 | 40 | SO4 |
| 4 | 100 | 0.43 | 0.78 | 23 | empty |
| 5 | 102 | 0.40 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4N7T · Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DTU0 · AlphaFold monomer V2.0 prediction for phosphopentomutase (Q8DTU0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8DTU0
- Elsewhere: RCSB PDB 4N7T · PDBe 4N7T · UniProt Q8DTU0
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