MolNFT v1 · #63553 · protein
Crystal structure of human selenophosphate synthetase 1 complex with ampcp
3FD5 · Selenide, water dikinase 1: “Crystal structure of human selenophosphate synthetase 1 complex with ampcp”. X-ray diffraction, 4 ligands (AP2, MG, K), 6 pockets (best druggability 0.83). MolNFT v1 #63553 on GenesisL1: 3D structure…
- PDB
- 3FD5
- Type
- protein
- Length
- 694 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
- AP2, MG, K, PO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenide, water dikinase 1 (EC 2.7.9.3) | protein | 339 | 36% helix, 26% strand | P49903 |
| B | Selenide, water dikinase 1 (EC 2.7.9.3) | protein | 355 | 35% helix, 25% strand | P49903 |
Ligands and binding sites
- AP2 · Phosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- K · Potassium 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.83 | 0.92 | 55 | AP2, PO4, MG, K |
| 2 | 419 | 0.82 | 0.90 | 57 | AP2, PO4, MG, K |
| 3 | 61 | 0.40 | 0.80 | 15 | empty |
| 4 | 61 | 0.40 | 0.80 | 18 | empty |
| 5 | 55 | 0.38 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2521 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3FD5 · Crystal structure of human selenophosphate synthetase 1 complex with AMPCP · 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 0.99
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 3FD5 · PDBe 3FD5 · UniProt P49903
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