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Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii

Analyse Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3FKG
Type
protein
Length
319 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, ZN, FE, CA
Pockets
1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AVersatile peroxidase VPL2 (EC 1.11.1.16)protein31942% helix, 7% strandO94753

Ligands and binding sites

  • HEM · Protoporphyrin IX containing Fe · ligand · chains A
  • ZN · Zinc ion · metal · 7 copies · chains A
  • FE · Fe (III) ion · metal · 3 copies · chains A
  • CA · Calcium ion · metal · 2 copies · chains A
  • CAC · Cacodylate ion · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14340.800.8845HEM, ZN

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

  • 3FKG · Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii · 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 1.00

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