MolNFT v1 · #119146 · protein
Crystal structure of fungal versatile peroxidase from pleurotus eryngii septuple mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R
5FNB · Versatile peroxidase VPL2: “Crystal structure of fungal versatile peroxidase from pleurotus eryngii septuple mutant E37K, H39R, V160A…”. X-ray diffraction, 3 ligands (HEM, CA, SO4), 4 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5FNB
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Versatile peroxidase VPL2
- EC
- 1.11.1.16, 1.11.1.7
- UniProt
- O94753
- Ligands
- HEM, CA, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Versatile peroxidase VPL2 (EC 1.11.1.16, 1.11.1.7) | protein | 329 | 41% helix, 8% strand | O94753 |
| B | Versatile peroxidase VPL2 (EC 1.11.1.16, 1.11.1.7) | protein | 315 | 43% helix, 7% strand | O94753 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.81 | 0.89 | 45 | HEM |
| 2 | 364 | 0.75 | 0.85 | 38 | HEM |
| 3 | 435 | 0.63 | 0.77 | 42 | SO4 |
| 4 | 235 | 0.51 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 366 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5FNB · Crystal structure of fungal versatile peroxidase from pleurotus eryngii septuple mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- O94753 · AlphaFold monomer V2.0 prediction for versatile peroxidase VPL2 (O94753) · a predicted model of the same protein · chain A 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 O94753
- Elsewhere: RCSB PDB 5FNB · PDBe 5FNB · UniProt O94753
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