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- PDB-1jq9: Crystal structure of a complex formed between phospholipase A2 fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jq9 | ||||||
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Title | Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / phospholipase A2 / Daboia russelli pulchella / neurotoxic / designed peptide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Betzel, C. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal Structure of a Complex Formed between a Snake Venom Phospholipase A2 and a Potent Peptide Inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 A Resolution Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Perbandt, M. / Srinivasan, A. / Betzel, C. / Singh, T.P. #1: ![]() Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 resolution Authors: Chandra, V. / Kaur, P. / SRINIVASAN, A. / Singh, T.P. #2: ![]() Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P. #3: ![]() Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between ...Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P. #4: ![]() Title: Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 A crystal structure Authors: Chandra, V. / Jasti, J. / Kaur, P. / Srinivasan, A. / Betzel, C. / Singh, T.P. #5: ![]() Title: Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Srinivasan, A. / Betzel, C. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.5 KB | Display | ![]() |
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Full document | ![]() | 401 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fe7 S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The two protein chains (A and B) represent the two molecules in the asymmetric unit, with the A molecule containing peptide inhibitor |
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Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein/peptide | | Mass: 657.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED. #3: Chemical | ChemComp-ACY / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 239988 / Num. obs: 239988 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.04 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 4.7 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1581 / Rsym value: 0.09 / % possible all: 98 |
Reflection | *PLUS Num. obs: 22959 / Num. measured all: 239988 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 98 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FE7 ![]() 1fe7 Resolution: 1.8→11.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2042260.78 / Data cutoff high rms absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0477 Å2 / ksol: 0.332842 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→11.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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