+Open data
-Basic information
Entry | Database: PDB / ID: 7agc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Protease Sapp1p from Candida parapsilosis in complex with KB74 | |||||||||
Components |
| |||||||||
Keywords | ANTIBIOTIC / Secreted aspartic protease / virulence factor / candidiasis / peptidomimetic inhibitors | |||||||||
Function / homology | Function and homology information candidapepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Candida parapsilosis (yeast) Streptomyces albus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Dostal, J. / Heidingsfeld, O. / Brynda, J. | |||||||||
Funding support | Czech Republic, 1items
| |||||||||
Citation | Journal: J Enzyme Inhib Med Chem / Year: 2021 Title: Structural determinants for subnanomolar inhibition of the secreted aspartic protease Sapp1p from Candida parapsilosis . Authors: Dostal, J. / Brynda, J. / Vankova, L. / Zia, S.R. / Pichova, I. / Heidingsfeld, O. / Lepsik, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7agc.cif.gz | 291.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7agc.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 7agc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7agc_validation.pdf.gz | 499.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7agc_full_validation.pdf.gz | 510.9 KB | Display | |
Data in XML | 7agc_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 7agc_validation.cif.gz | 88.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/7agc ftp://data.pdbj.org/pub/pdb/validation_reports/ag/7agc | HTTPS FTP |
-Related structure data
Related structure data | 7agbC 7agdC 7ageC 3fv3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 8 molecules ABDFEICG
#1: Protein | Mass: 35865.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: SAPP1 / Production host: Candida parapsilosis (yeast) / References: UniProt: B8YPM3, candidapepsin #2: Protein/peptide | Mass: 841.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Streptomyces albus (bacteria) |
---|
-Non-polymers , 5 types, 1063 molecules
#3: Chemical | ChemComp-MES / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-FOR / #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100-fold molar inhibitor excess, Cpr=20mg/ml; drops: 0.002ml protein + 0.001ml reservoir; reservoir: 0.1M MES pH 6.5, 30% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→78.84 Å / Num. obs: 253539 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.064 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.443 / Num. unique obs: 38187 / CC1/2: 0.78 / Rrim(I) all: 0.537 / % possible all: 0.903 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FV3 Resolution: 1.35→78.84 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.894 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.79 Å2 / Biso mean: 11.426 Å2 / Biso min: 4.51 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→78.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|