4ZAR | pdb_00004zar

Crystal Structure of Proteinase K from Engyodontium albuminhibited by METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE at 1.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4ZAR/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Parengyodontium album, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-14 Released: 2015-05-06 
• Deposition Author(s): Sawaya, M.R., Cascio, D., Collazo, M., Bond, C., Cohen, A., DeNicola, A., Eden, K., Jain, K., Leung, C., Lubock, N., McCormick, J., Rosinski, J., Spiegelman, L., Athar, Y., Tibrewal, N., Winter, J., Solomon, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.135 (Depositor), 0.135 (DCC) 
• R-Value Work: 
  0.110 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Proteinase K from Engyodontium album inhibited by METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE at 1.15 A resolution

Sawaya, M.R., Cascio, D., Collazo, M., Bond, C., Cohen, A., DeNicola, A., Eden, K., Jain, K., Leung, C., Lubock, N., McCormick, J., Rosinski, J., Spiegelman, L., Athar, Y., Tibrewal, N., Winter, J., Solomon, S.

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: 29.59 kDa 
• Atom Count: 2,483 
• 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): 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
METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE, bound form	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCS	B	L-PEPTIDE LINKING	C10 H12 Cl N O		PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002159	B	METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.135 (Depositor), 0.135 (DCC) 
• R-Value Work:  0.110 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.85	α = 90
b = 67.85	β = 90
c = 102.51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Sawaya, M.R., Cascio, D., Collazo, M., Bond, C., Cohen, A., DeNicola, A., Eden, K., Jain, K., Leung, C., Lubock, N., McCormick, J., Rosinski, J., Spiegelman, L., Athar, Y., Tibrewal, N., Winter, J., Solomon, S.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description