MolNFT v1 · #32348 · protein
The structure of hydroxypropylphosphonic acid epoxidase from S. wedmorenis.
2BNO: “The structure of hydroxypropylphosphonic acid epoxidase from S. wedmorenis.”. X-ray diffraction, 3 ligands (HG, ZN, SO4), 5 pockets (best druggability 0.61). MolNFT v1 #32348 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2BNO
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxidase
- UniProt
- Q56185
- Ligands
- HG, ZN, SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxidase | protein | 191 | 28% helix, 26% strand | Q56185 |
| B | Epoxidase | protein | 194 | 26% helix, 29% strand | Q56185 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.61 | 0.78 | 36 | SO4 |
| 2 | 271 | 0.57 | 0.78 | 34 | SO4 |
| 3 | 126 | 0.43 | 0.76 | 28 | HG |
| 4 | 98 | 0.36 | 0.75 | 18 | empty |
| 5 | 69 | 0.35 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1548 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2BNO · The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis. · the same entry in another collection · chain A against A, TM-score 1.00
- Q56185 · AlphaFold monomer V2.0 prediction for (S)-2-hydroxypropylphosphonic acid epoxidase… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q56185
- Elsewhere: RCSB PDB 2BNO · PDBe 2BNO · UniProt Q56185
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