5CW1 | pdb_00005cw1

Proteinase K complexed with 4-iodopyrazole

• PDB DOI: https://doi.org/10.2210/pdb5CW1/pdb

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


• Deposited: 2015-07-27 Released: 2015-12-30 
• Deposition Author(s): Bauman, J.D., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Rapid experimental SAD phasing and hot spot identification with halogenated fragments

Bauman, J.D., Harrison, J.J.E.K., Arnold, E.

(2016) IUCrJ 3: 51-60

• DOI: https://doi.org/10.1107/S2052252515021259

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: 29.99 kDa 
• Atom Count: 2,464 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYZ	D [auth A], E [auth A], F [auth A]	4-IODOPYRAZOLE C3 H3 I N2 LLNQWPTUJJYTTE-UHFFFAOYSA-N
IOD	G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.017	α = 90
b = 68.017	β = 90
c = 102.045	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Bauman, J.D., Arnold, E.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary