3FJW

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

• PDB DOI: https://doi.org/10.2210/pdb3FJW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pleurotus eryngii
• Mutation(s): No 


• Deposited: 2008-12-15 Released: 2009-12-15 
• Deposition Author(s): Piontek, K., Martinez, A.T., Choinowski, T., Plattner, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.158 
• R-Value Observed: 0.163 

Literature

Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates

Piontek, K., Choinowski, T., Perez-Boada, M., Ruiz-Duenas, F.J., Martinez, M.J., Plattner, D.A., Martinez, A.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.92 kDa 
• Atom Count: 5,548 
• Modelled Residue Count: 662 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Versatile peroxidase VPL2	A, B	331	Pleurotus eryngii	Mutation(s): 0  EC: 1.11.1.16
UniProt
Find proteins for O94753 (Pleurotus eryngii) Explore O94753  Go to UniProtKB:  O94753

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G09507TI GlyCosmos:  G09507TI GlyGen:  G09507TI

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], M [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	I [auth A], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
MN	H [auth A], P [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	F [auth A], G [auth A], N [auth B], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.158 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.141	α = 90
b = 92.762	β = 90
c = 113.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Piontek, K., Martinez, A.T., Choinowski, T., Plattner, D.A.

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary