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Yorodumi- PDB-1mf4: Structure-based design of potent and selective inhibitors of phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mf4 | ||||||
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Title | Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Naja naja sagittifera / phospholipase A2 / designed inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Naja sagittifera (cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Singh, R.K. / Vikram, P. / Paramsivam, M. / Jabeen, T. / Sharma, S. / Makker, J. / Dey, S. / Kaur, P. / Srinivasan, A. / Singh, T.P. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor ...Title: Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) at 1.9 A resolution reveals unique features Authors: Singh, R.K. / Vikram, P. / Makker, J. / Jabeen, T. / Sharma, S. / Dey, S. / Kaur, P. / Srinivasan, A. / Singh, T.P. #1: Journal: To be Published Title: Crystal Structure of an Acidic Phospholipase A2 from Naja naja sagittifera at 1.5 A Resolution Authors: Singh, R.K. / Sharma, S. / Jabeen, T. / Kaur, P. / Singh, T.P. #2: Journal: To be Published Title: Crystal Structure of a New Isoform of Phospholipase A2 from Naja naja sagittifera at 1.6 A Resolution Authors: Singh, R.K. / Vikram, P. / Paramasivam, M. / Jabeen, T. / Sharma, S. / Kaur, P. / Srinivasan, A. / 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 | 1mf4.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mf4.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mf4 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mf4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ln8S S: Starting model for refinement |
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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: 13128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: Venom / References: UniProt: P60045, phospholipase A2 |
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#2: Protein/peptide | Mass: 579.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized. |
#3: Chemical | ChemComp-CA / |
#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: 2.26 Å3/Da / Density % sol: 45.1 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / pH: 6 Details: sodium phosphate, CaCl2, ethanol; Co-crystallation of protein: peptide in 1:10 molar ratio, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.00 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 298 K / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2001 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 8247 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 1.04 % / Biso Wilson estimate: 20.63 Å2 / Rsym value: 0.073 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.289 / % possible all: 61.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 92 % / Num. measured all: 8668 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 61.3 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LN8 Resolution: 1.9→19.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.811 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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