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Yorodumi- PDB-2fnx: Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2):... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fnx | ||||||
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Title | Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution | ||||||
Components |
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Keywords | HYDROLASE / peptide inhibitor complex | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Singh, N. / Srivastava, P. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution Authors: Singh, N. / Srivastava, P. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fnx.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fnx.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fnx ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fnx | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 |
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#2: Protein/peptide | Mass: 430.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized peptide |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.2M ammonoium sulfate, 30% PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 2005 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→52.7 Å / Num. all: 3181 / Num. obs: 3181 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.7→2.73 Å / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→52.7 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.465 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.879 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→52.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.702→2.772 Å / Total num. of bins used: 20 /
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