7AGE

Protease Sapp1p from Candida parapsilosis in complex with KB32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural determinants for subnanomolar inhibition of the secreted aspartic protease Sapp1p from Candida parapsilosis .

Dostal, J.Brynda, J.Vankova, L.Zia, S.R.Pichova, I.Heidingsfeld, O.Lepsik, M.

(2021) J Enzyme Inhib Med Chem 36: 914-921

  • DOI: https://doi.org/10.1080/14756366.2021.1906664
  • Primary Citation of Related Structures:  
    7AGB, 7AGC, 7AGD, 7AGE

  • PubMed Abstract: 

    Pathogenic Candida albicans yeasts frequently cause infections in hospitals. Antifungal drugs lose effectiveness due to other Candida species and resistance. New medications are thus required. Secreted aspartic protease of C. parapsilosis (Sapp1p) is a promising target. We have thus solved the crystal structures of Sapp1p complexed to four peptidomimetic inhibitors. Three potent inhibitors (K i : 0.1, 0.4, 6.6 nM) resembled pepstatin A (K i : 0.3 nM), a general aspartic protease inhibitor, in terms of their interactions with Sapp1p. However, the weaker inhibitor (K i : 14.6 nM) formed fewer nonpolar contacts with Sapp1p, similarly to the smaller HIV protease inhibitor ritonavir (K i : 1.9 µM), which, moreover, formed fewer H-bonds. The analyses have revealed the structural determinants of the subnanomolar inhibition of C. parapsilosis aspartic protease. Because of the high similarity between Saps from different Candida species, these results can further be used for the design of potent and specific Sap inhibitor-based antimycotic drugs.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CandidapepsinA,
C [auth B],
E [auth D],
G [auth F]
339Candida parapsilosisMutation(s): 0 
Gene Names: SAPP1
EC: 3.4.23.24
UniProt
Find proteins for P32951 (Candida parapsilosis)
Explore P32951 
Go to UniProtKB:  P32951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32951
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PepstatinB [auth I],
D [auth C],
F [auth E],
H [auth G]
7synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth D]
M [auth D]
I [auth B],
J [auth B],
K [auth B],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth F],
S [auth F],
T [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PSA
Query on PSA
B [auth I],
D [auth C],
F [auth E],
H [auth G]
PEPTIDE-LIKEC11 H15 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.26α = 90
b = 87.29β = 90
c = 157.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Czech Republic)Czech RepublicCZ.02.1.01/0.0/16_019/000729

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description