[English] 日本語
Yorodumi- PDB-2gns: Design of specific peptide inhibitors of phospholipase A2: Crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gns | ||||||
---|---|---|---|---|---|---|---|
Title | Design of specific peptide inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II phospholipase A2 and a designed pentapeptide Ala- Leu- Val- Tyr- Lys at 2.3 A resolution | ||||||
Components |
| ||||||
Keywords | HYDROLASE / peptide inhibitor / binding constant | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Singh, N. / Sharma, S. / Somvanshi, R.K. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Design of specific peptide inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II phospholipase A2 and a designed pentapeptide Ala - Leu - Val - Tyr - Lys at 2.3 A resolution Authors: Singh, N. / Sharma, S. / Somvanshi, R.K. / Dey, S. / Singh, T.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gns.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gns.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gns ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gns | HTTPS FTP |
---|
-Related structure data
Related structure data | 1fb2S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Protein/peptide | Mass: 593.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chmically synthesized |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.2 Details: 0.2M ammonium sulphate, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 288 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 22, 2006 / 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: 2.3→20 Å / Num. all: 5989 / Num. obs: 5989 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.6 Å2 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 94.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FB2.pdb Resolution: 2.3→18.79 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 73313.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.3662 Å2 / ksol: 0.385958 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→18.79 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|