Research workbench
The crystal structure of selenophosphate synthetase from E. COLI
Analyse The crystal structure of selenophosphate synthetase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U0O
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenide, water dikinase
- EC
- 2.7.9.3
- UniProt
- P16456
- Ligands
- MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenide, water dikinase (EC 2.7.9.3) | protein | 319 | 35% helix, 24% strand | P16456 |
| B | Selenide, water dikinase (EC 2.7.9.3) | protein | 335 | 34% helix, 24% strand | P16456 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.81 | 0.83 | 101 | empty |
| 2 | 734 | 0.70 | 0.77 | 90 | empty |
| 3 | 60 | 0.39 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2396 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3U0O · The crystal structure of selenophosphate synthetase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P16456 · AlphaFold monomer V2.0 prediction for selenide, water dikinase (P16456) · a predicted model of the same protein · chain A 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 P16456
- Elsewhere: RCSB PDB 3U0O · PDBe 3U0O · UniProt P16456
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