1P7W | pdb_00001p7w

Crystal structure of the complex of Proteinase K with a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb1P7W/pdb

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


• Deposited: 2003-05-06 Released: 2004-05-18 
• Deposition Author(s): Bilgrami, S., Perbandt, M., Chandra, V., Banumathi, S., Kaur, P., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.142 (Depositor) 
• R-Value Work: 
  0.129 (Depositor) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of Proteinase K with heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution

Bilgrami, S., Perbandt, M., Chandra, V., Banumathi, S., Kaur, P., Betzel, C., 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: 30.01 kDa 
• Atom Count: 2,531 
• Modeled Residue Count: 286 
• Deposited Residue Count: 286 
• 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
inhibitor peptide	B	7	N/A	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.142 (Depositor) 
• R-Value Work:  0.129 (Depositor) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.835	α = 90
b = 67.835	β = 90
c = 101.563	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Bilgrami, S., Perbandt, M., Chandra, V., Banumathi, S., Kaur, P., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary