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Yorodumi- PDB-6ycf: Structure the bromelain protease from Ananas comosus in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ycf | ||||||
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Title | Structure the bromelain protease from Ananas comosus in complex with the E64 inhibitor | ||||||
Components | FBSB | ||||||
Keywords | HYDROLASE / cysteine protease / stem bromelain protein | ||||||
Function / homology | Function and homology information proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Ananas comosus (pineapple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Azarkan, M. / Charlier, P. / Herman, R. / Delbrassine, F. / Sauvage, E. / M Rabet, N. / Calvo Esposito, R. / Kerff, F. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Structures of the free and inhibitors-bound forms of bromelain and ananain from Ananas comosus stem and in vitro study of their cytotoxicity. Authors: Azarkan, M. / Maquoi, E. / Delbrassine, F. / Herman, R. / M'Rabet, N. / Calvo Esposito, R. / Charlier, P. / Kerff, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ycf.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ycf.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ycf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ycf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6ycf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ycf_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6ycf_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/6ycf ftp://data.pdbj.org/pub/pdb/validation_reports/yc/6ycf | HTTPS FTP |
-Related structure data
Related structure data | 6y6lC 6ycbC 6yccC 6ycdC 6yceSC 6ycgC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 216 / Label seq-ID: 2 - 216
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23317.342 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) Plasmid details: residues G84, N99 and S210 were refined in alternate conformation with A1084, D1099 and P1210 in accordance with electron density and mass spectrometry results References: UniProt: O23799, UniProt: A0A199VSS3*PLUS |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 375 molecules
#3: Chemical | #4: Chemical | ChemComp-CIT / | #6: Chemical | ChemComp-IPA / | #7: 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: 2.86 Å3/Da / Density % sol: 57.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 4000, 20% 2-propanol, 0.1 M citrate pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→45.36 Å / Num. obs: 47074 / % possible obs: 98.2 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Net I/σ(I): 14.6 / Num. measured all: 587741 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YCE Resolution: 1.85→41.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.318 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.05 Å2 / Biso mean: 29.032 Å2 / Biso min: 16.01 Å2
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Refinement step | Cycle: final / Resolution: 1.85→41.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7025 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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