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Yorodumi- PDB-1zm6: Crystal structure of the complex formed beween a group I phosphol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zm6 | ||||||
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Title | Crystal structure of the complex formed beween a group I phospholipase A2 and designed penta peptide Leu-Ala-Ile-Tyr-Ser at 2.6A resolution | ||||||
Components |
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Keywords | HYDROLASE / peptide design / inhibitor | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Naja sagittifera (cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Singh, R.K. / Singh, N. / Jabeen, T. / Sharma, S. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: J.Drug Target. / Year: 2005 Title: Crystal structure of the complex of group I PLA2 with a group II-specific peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) at 2.6 A resolution. Authors: Singh, R.K. / Singh, N. / Jabeen, T. / 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 | 1zm6.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zm6.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zm6 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zm6 | HTTPS FTP |
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-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: 13172.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: P60045, phospholipase A2 | ||
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#2: Protein/peptide | Mass: 565.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized. | ||
#3: Chemical | #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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10mM phosphate buffer, 20% ethenol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2003 / Details: mirror |
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: 2.6→20 Å / Num. all: 3306 / Num. obs: 3306 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.7 Å2 |
Reflection shell | Resolution: 2.6→2.65 Å / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.36 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 721920.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.7932 Å2 / ksol: 0.409735 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.36 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.6 Å / Total num. of bins used: 6 /
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Xplor file |
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