Research workbench
Direct-evolutioned unspecific peroxygenase from agrocybe aegerita, in complex with acetate
Analyse Direct-evolutioned unspecific peroxygenase from agrocybe aegerita, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OXT
- Type
- protein
- Length
- 981 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unspecific peroxygenase
- EC
- 1.11.2.1
- UniProt
- B9W4V6
- Ligands
- HEM, NAG, MG, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Unspecific peroxygenase (EC 1.11.2.1) | protein | 327 | 43% helix, 6% strand | B9W4V6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.85 | 0.89 | 55 | HEM, ACT |
| 2 | 622 | 0.84 | 0.88 | 58 | HEM, ACT |
| 3 | 629 | 0.84 | 0.88 | 58 | HEM, ACT |
| 4 | 528 | 0.66 | 0.77 | 52 | ACT |
| 5 | 130 | 0.47 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 449 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 5OXT · Direct-evolutioned unspecific peroxygenase from agrocybe aegerita, in complex with acetate · the same entry in another collection · chain A against A, TM-score 1.00
- B9W4V6 · AlphaFold monomer V2.0 prediction for aromatic peroxygenase (B9W4V6) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 B9W4V6
- Elsewhere: RCSB PDB 5OXT · PDBe 5OXT · UniProt B9W4V6
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