4YBF | pdb_00004ybf

Aspartic Proteinase Sapp2 Secreted from Candida Parapsilosis at 1.25 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4YBF/pdb

• Classification: HYDROLASE
• Organism(s): Candida parapsilosis CDC317
• Expression System: Candida parapsilosis
• Mutation(s): No 


• Deposited: 2015-02-18 Released: 2016-01-27 
• Deposition Author(s): Dostal, J., Hruskova-Heidingsfeldova, O., Rezacova, P., Brynda, J., Mareckova, L., Pichova, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.174 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.147 (Depositor) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Dostal, J., Pecina, A., Hruskova-Heidingsfeldova, O., Mareckova, L., Pichova, I., Rezacova, P., Lepsik, M., Brynda, J.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2494-2504

• PubMed: 26627656 
• DOI: https://doi.org/10.1107/S1399004715019392
• Primary Citation Related Structures: 
  4Y9W, 4YBF


• PubMed Abstract: 
  

  The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

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Organizational Affiliation: 
• Institute of Organic Chemistry and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.58 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 334 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Candidapepsin-2	A	334	Candida parapsilosis CDC317	Mutation(s): 0  Gene Names: CPAR2_102580 EC: 3.4.23.24
UniProt
Find proteins for G8B6Y8 (Candida parapsilosis (strain CDC 317 / ATCC MYA-4646)) Explore G8B6Y8  Go to UniProtKB:  G8B6Y8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.174 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.147 (Depositor) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.138	α = 90
b = 57.147	β = 90.61
c = 54.553	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Dostal, J., Hruskova-Heidingsfeldova, O., Rezacova, P., Brynda, J., Mareckova, L., Pichova, I.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary