9KW1 | pdb_00009kw1

Crystal structure of proteinase K from Engyodontium album

• PDB DOI: https://doi.org/10.2210/pdb9KW1/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Expression System: Parengyodontium album
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-10 
• Deposition Author(s): Sugahara, M., Maki-Yonekura, S., Yonekura, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of proteinase K from Engyodontium album

Sugahara, M., Maki-Yonekura, S., Yonekura, K.

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)

Macromolecule Content 

• Total Structure Weight: 29.32 kDa 
• Atom Count: 2,285 
• Modeled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0  Gene Names: PROK EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EU (Subject of Investigation/LOI)	B [auth A], C [auth A]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N
NO3 (Subject of Investigation/LOI)	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.7	α = 90
b = 68.7	β = 90
c = 108.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling
SHELXCD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Sugahara, M., Maki-Yonekura, S., Yonekura, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release