MolNFT v1 · #123883 · protein
An iron-bound structure of the salicylate synthase IRP9
5JY9 · Putative salicylate synthetase: “An iron-bound structure of the salicylate synthase IRP9”. X-ray diffraction, 2 ligands (FE2, SO4), 9 pockets (best druggability 0.81). MolNFT v1 #123883 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JY9
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative salicylate synthetase
- UniProt
- A1JTF3
- Ligands
- FE2, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative salicylate synthetase | protein | 401 | 30% helix, 34% strand | A1JTF3 |
| B | Putative salicylate synthetase | protein | 424 | 32% helix, 34% strand | A1JTF3 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.81 | 0.97 | 33 | SO4, ACT |
| 2 | 51 | 0.71 | 0.99 | 22 | ACT |
| 3 | 104 | 0.45 | 0.79 | 22 | empty |
| 4 | 60 | 0.45 | 0.83 | 13 | empty |
| 5 | 50 | 0.44 | 0.84 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 807 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JY9 · An iron-bound structure of the salicylate synthase Irp9 · the same entry in another collection · chain A against A, TM-score 1.00
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 A1JTF3
- Elsewhere: RCSB PDB 5JY9 · PDBe 5JY9 · UniProt A1JTF3
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