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Yorodumi- PDB-1f2b: CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SULFONE DERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f2b | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SULFONE DERIVED INHIBITOR (III) | ||||||
Components | CRUZAIN | ||||||
Keywords | HYDROLASE / cysteine protease / covalent inhibitor / vinyl sulfone-derived / P1' pocket | ||||||
Function / homology | Function and homology information cruzipain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Brinen, L.S. / Hansell, E. / Roush, W.R. / McKerrow, J.H. / Fletterick, R.J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A target within the target: probing cruzain's P1' site to define structural determinants for the Chagas' disease protease. Authors: Brinen, L.S. / Hansell, E. / Cheng, J. / Roush, W.R. / McKerrow, J.H. / Fletterick, R.J. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The Crystal Structure of Cruzain: a Therapeutic Target for Chagas' Disease Authors: McGrath, M.E. / Eakin, A.E. / Engel, J.C. / McKerrow, J.H. / Craik, C.S. / Fletterick, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f2b.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f2b.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f2b_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 1f2b_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 1f2b_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1f2b_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/1f2b ftp://data.pdbj.org/pub/pdb/validation_reports/f2/1f2b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: DH5ALPHA / Production host: Escherichia coli (E. coli) References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-VS3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.09 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Sodium citrate; micro seeding, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 5.8 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 17495 / Num. obs: 15513 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.22 / % possible all: 74.4 |
Reflection shell | *PLUS % possible obs: 74.4 % |
-Processing
Software |
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Refinement | Resolution: 1.8→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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