2DUJ | pdb_00002duj

Crystal structure of the complex formed between proteinase K and a synthetic peptide Leu-Leu-Phe-Asn-Asp at 1.67 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2DUJ/pdb

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


• Deposited: 2006-07-23 Released: 2006-08-08 
• Deposition Author(s): Singh, A.K., Singh, N., Somvanshi, R.K., Gupta, D., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.192 (Depositor) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of proteinase K with a specific lactoferrin peptide Val-Leu-Leu-His at 1.93 A resolution

Singh, A.K., Singh, N., Somvanshi, R.K., Gupta, D., Sharma, S., Bhushan, A., Dey, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 29.68 kDa 
• Atom Count: 2,382 
• Modelled Residue Count: 284 
• Deposited Residue Count: 284 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LLFND	B [auth P]	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.192 (Depositor) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.249	α = 90
b = 68.249	β = 90
c = 108.241	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Singh, A.K., Singh, N., Somvanshi, R.K., Gupta, D., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary