MolNFT v1 · #135647 · protein
PSF4 in complex with FE2+ and (R)-2-hpp
5U58 · (S)-2-hydroxypropylphosphonic acid epoxidase: “PSF4 in complex with FE2+ and (R)-2-hpp”. X-ray diffraction, 2 ligands (TB6, FE), 10 pockets (best druggability 0.47). MolNFT v1 #135647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U58
- Type
- protein
- Length
- 712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-2-hydroxypropylphosphonic acid epoxidase
- EC
- 1.11.1.23
- UniProt
- Q9JN69
- Ligands
- TB6, FE
- Pockets
- 10 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 190 | 15% helix, 37% strand | Q9JN69 |
| B | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 186 | 15% helix, 39% strand | Q9JN69 |
| C | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 162 | 14% helix, 38% strand | Q9JN69 |
| D | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 174 | 18% helix, 40% strand | Q9JN69 |
Ligands and binding sites
- TB6 · [(2R)-2-hydroxypropyl]phosphonic acid · ligand · 2 copies · chains A, D, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.47 | 0.76 | 26 | empty |
| 2 | 101 | 0.40 | 0.77 | 26 | empty |
| 3 | 89 | 0.36 | 0.76 | 22 | empty |
| 4 | 73 | 0.36 | 0.77 | 17 | empty |
| 5 | 71 | 0.32 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1896 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1829 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1578 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1360 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 Q9JN69
- Elsewhere: RCSB PDB 5U58 · PDBe 5U58 · UniProt Q9JN69
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.