6K8M | pdb_00006k8m

High resolution crystal structure of proteinase K with thiourea

• PDB DOI: https://doi.org/10.2210/pdb6K8M/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-13 Released: 2019-12-25 
• Deposition Author(s): Ahmad, M.S., Akbar, Z., Choudhary, M.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

High resolution crystal structure of proteinase K with thiourea

Ahmad, M.S., Akbar, Z., Choudhary, M.I.

(2019) Bioorganic Chemistry 

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: 2,269 
• 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 [auth E]	279	Parengyodontium album	Mutation(s): 1  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
SO4	E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
TOU (Subject of Investigation/LOI)	B [auth E], C [auth E], D [auth E]	THIOUREA C H4 N2 S UMGDCJDMYOKAJW-UHFFFAOYSA-N
CL	F [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.842	α = 90
b = 67.842	β = 90
c = 102.377	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Ahmad, M.S., Akbar, Z., Choudhary, M.I.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary