MolNFT v2 · #219116 · protein
Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with lauric acid
8RNL: “Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with lauric acid”. X-ray diffraction at 1.6, 5 ligands (DAO, HEM, NAG), 5 pockets (best druggability 0.82). MolNFT v2 #219116 on GenesisL1: 3D structure…
- PDB
- 8RNL
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Marasmius wettsteinii
- Molecule
- Unspecific peroxygenase
- EC
- 1.11.2.1
- Ligands
- DAO, HEM, NAG, MG, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 46% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Unspecific peroxygenase (EC 1.11.2.1) | protein | 240 | 46% helix, 5% strand | — |
Ligands and binding sites
- DAO · Lauric acid · ligand · 3 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
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 | 520 | 0.82 | 0.88 | 47 | HEM, DAO |
| 2 | 610 | 0.81 | 0.86 | 72 | DAO, HEM |
| 3 | 67 | 0.41 | 0.81 | 18 | empty |
| 4 | 63 | 0.37 | 0.79 | 14 | empty |
| 5 | 63 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 disulfide (N-glycosylation, disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8RNL · PDBe 8RNL
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