Research workbench
Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate
Analyse Crystal structure of human selenophosphate synthetase 1 complex with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FD6
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenide, water dikinase 1
- EC
- 2.7.9.3
- UniProt
- P49903
- Ligands
- ADP, MG, NA, PO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenide, water dikinase 1 (EC 2.7.9.3) | protein | 342 | 35% helix, 26% strand | P49903 |
| B | Selenide, water dikinase 1 (EC 2.7.9.3) | protein | 353 | 35% helix, 25% strand | P49903 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.82 | 0.89 | 68 | ADP, PO4, MG, NA |
| 2 | 128 | 0.77 | 0.95 | 25 | PO4 |
| 3 | 247 | 0.76 | 0.90 | 35 | ADP, PO4, MG, NA |
| 4 | 59 | 0.52 | 0.87 | 16 | empty |
| 5 | 107 | 0.39 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2604 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3FD6 · Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P49903 · AlphaFold monomer V2.0 prediction for selenide, water dikinase 1 (P49903) · 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 P49903
- Elsewhere: RCSB PDB 3FD6 · PDBe 3FD6 · UniProt P49903
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