2PQ2 | pdb_00002pq2

Structure of serine proteinase K complex with a highly flexible hydrophobic peptide at 1.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PQ2/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Mutation(s): Yes 


• Deposited: 2007-05-01 Released: 2007-05-29 
• Deposition Author(s): Ethayathulla, A.S., Singh, A.K., Singh, N., Sharma, S., Sinha, M., Somvanshi, R.K., Kaur, P., Dey, S., Srinivasan, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.207 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure of serine proteinase K complex with a highly flexible hydrophobic peptide at 1.8A resolution

Ethayathulla, A.S., Singh, A.K., Singh, N., Sharma, S., Sinha, M., Somvanshi, R.K., Kaur, P., Dey, S., Srinivasan, A., 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.

Macromolecule Content 

• Total Structure Weight: 29.45 kDa 
• Atom Count: 2,357 
• Modeled 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): 1  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
GALAG peptide	B	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: 1.82 Å
• R-Value Free:  0.207 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.314	α = 90
b = 68.314	β = 90
c = 108.418	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Ethayathulla, A.S., Singh, A.K., Singh, N., Sharma, S., Sinha, M., Somvanshi, R.K., Kaur, P., Dey, S., Srinivasan, A., Singh, T.P.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary