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
- 5FUK
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mroupo
- EC
- 1.11.2.1
- Ligands
- HEM, SNP, PLM, RNP, NAG, MAN, BMA, MG, PO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mroupo (EC 1.11.2.1) | protein | 234 | 46% helix, 5% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SNP · 1-(isopropylamino)-3-(1-naphthyloxy)-2-propanol · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- RNP · (1E,2R)-1-(isopropylimino)-3-(1-naphthyloxy)propan-2-ol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
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 | 488 | 0.82 | 0.88 | 48 | HEM, SNP, PLM, RNP |
| 2 | 504 | 0.81 | 0.87 | 51 | HEM, SNP, PLM, RNP |
| 3 | 72 | 0.43 | 0.81 | 23 | empty |
| 4 | 84 | 0.42 | 0.79 | 23 | empty |
| 5 | 56 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FUK · 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 5FUK · PDBe 5FUK
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