MolNFT v1 · #113309 · protein
Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii. mutant vpi. mutated residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.
5ABN · Versatile peroxidase VPL2: “Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii. mutant vpi. mutated…”. X-ray diffraction, 3 ligands (HEM, CA, MG), 3 pockets (best druggability 0.81). MolNFT v1 #113309…
- 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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