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Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii. mutant vpi. mutated residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.
Analyse Crystal structure analysis of fungal versatile peroxidase from pleurotus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABN
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Versatile peroxidase VPL2
- EC
- 1.11.1.16
- UniProt
- O94753
- Ligands
- HEM, CA, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Versatile peroxidase VPL2 (EC 1.11.1.16) | protein | 326 | 42% helix, 7% strand | O94753 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.81 | 0.89 | 49 | HEM, MG |
| 2 | 85 | 0.60 | 0.88 | 21 | empty |
| 3 | 114 | 0.45 | 0.78 | 24 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5ABN · CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. 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 5ABN · PDBe 5ABN · UniProt O94753
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