Research workbench
Crystallization of a dimeric heme peroxygenase from the fungus marasmius rotula
Analyse Crystallization of a dimeric heme peroxygenase from the fungus marasmius rotula in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUJ
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mroupo
- EC
- 1.11.2.1
- Ligands
- HEM, NAG, BMA, MAN, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mroupo (EC 1.11.2.1) | protein | 236 | 45% helix, 5% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.82 | 0.88 | 56 | HEM, ACT |
| 2 | 579 | 0.82 | 0.87 | 59 | HEM, ACT |
| 3 | 67 | 0.40 | 0.80 | 23 | empty |
| 4 | 54 | 0.39 | 0.81 | 14 | empty |
| 5 | 71 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 939 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FUJ · Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5FUJ · PDBe 5FUJ
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