+Open data
-Basic information
Entry | Database: PDB / ID: 8gt0 | ||||||
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Title | Structure of falcipain and human Stefin A complex | ||||||
Components |
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Keywords | HYDROLASE / falcipain / stefin / complex | ||||||
Function / homology | Function and homology information negative regulation of peptidase activity / peptidase inhibitor complex / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / proteolysis involved in protein catabolic process / negative regulation of proteolysis ...negative regulation of peptidase activity / peptidase inhibitor complex / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / proteolysis involved in protein catabolic process / negative regulation of proteolysis / cell-cell adhesion / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / extracellular space / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | ||||||
Authors | Chakraborty, S. / Biswas, S. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Structure of falcipain and human Stefin A complex Authors: Chakraborty, S. / Biswas, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gt0.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gt0.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/8gt0 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/8gt0 | HTTPS FTP |
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-Related structure data
Related structure data | 8gt7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 5 molecules ACEBD
#1: Protein | Mass: 27205.672 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Escherichia coli (E. coli) References: UniProt: Q8I6U4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 11020.464 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSTA, STF1, STFA / Production host: Escherichia coli (E. coli) / References: UniProt: P01040 |
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-Non-polymers , 9 types, 320 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PE8 / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PG4 / #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5, 1.0 M sodium acetate and 5 mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 3.28→43.99 Å / Num. obs: 14644 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.1 Å2 / Rmerge(I) obs: 0.428 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.28→3.4 Å / Num. unique obs: 1449 / CC1/2: 0.568 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→43.99 Å / SU ML: 0.5084 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.0269 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.28→43.99 Å
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Refine LS restraints |
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LS refinement shell |
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