MolNFT v1 · #32346 · protein
The structure of hydroxypropylphosphonic acid epoxidase from S. wedmorenis.
2BNM: “The structure of hydroxypropylphosphonic acid epoxidase from S. wedmorenis.”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.70). MolNFT v1 #32346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BNM
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxidase
- UniProt
- Q56185
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epoxidase | protein | 194 | 28% helix, 26% strand | Q56185 |
Ligands and binding sites
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 | 320 | 0.70 | 0.83 | 38 | ZN, SO4 |
| 2 | 339 | 0.61 | 0.78 | 43 | SO4 |
| 3 | 125 | 0.40 | 0.75 | 22 | empty |
| 4 | 101 | 0.39 | 0.76 | 21 | empty |
| 5 | 68 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1717 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2BNM · The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis. · the same entry in another collection · chain B against B, 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 0.89
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 2BNM · PDBe 2BNM · UniProt Q56185
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