MolNFT v1 · #135644 · protein
PSF4 in complex with MN2+ and (S)-2-hpp
5U55 · (S)-2-hydroxypropylphosphonic acid epoxidase: “PSF4 in complex with MN2+ and (S)-2-hpp”. X-ray diffraction, 2 ligands (S0H, MN), 13 pockets (best druggability 0.45). MolNFT v1 #135644 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U55
- Type
- protein
- Length
- 745 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
- S0H, MN
- Pockets
- 13 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 187 | 17% helix, 39% strand | Q9JN69 |
| B, C, D | (S)-2-hydroxypropylphosphonic acid epoxidase (EC 1.11.1.23) | protein | 186 | 17% helix, 40% strand | Q9JN69 |
Ligands and binding sites
- S0H · (S)-2-hydroxypropylphosphonic acid · ligand · 4 copies · chains A, D, B, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.45 | 0.82 | 23 | MN, S0H |
| 2 | 101 | 0.41 | 0.77 | 19 | empty |
| 3 | 107 | 0.38 | 0.75 | 24 | empty |
| 4 | 111 | 0.37 | 0.75 | 23 | empty |
| 5 | 99 | 0.36 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1849 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1840 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1459 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1353 Ų buried · 9 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 5U55 · PDBe 5U55 · UniProt Q9JN69
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