Research workbench
Direct-evolutioned unspecific peroxygenase from agrocybe aegerita, in complex with naphthalene
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
- 6EKW
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic peroxygenase
- EC
- 1.11.2.1
- UniProt
- B9W4V6
- Ligands
- HEM, NPY, NAG, MG, CL, PO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic peroxygenase (EC 1.11.2.1) | protein | 325 | 42% helix, 6% strand | B9W4V6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NPY · Naphthalene · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
- MOH · Methanol · additive · 15 copies · chains A
- GOL · Glycerol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.82 | 0.86 | 55 | HEM, NPY, MOH |
| 2 | 117 | 0.45 | 0.78 | 21 | empty |
| 3 | 54 | 0.27 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 5 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6EKW · Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with… · 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 A against A, TM-score 1.00
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 6EKW · PDBe 6EKW · UniProt B9W4V6
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