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Yorodumi- PDB-3h1x: Simultaneous inhibition of anti-coagulation and inflammation: Cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h1x | ||||||
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Title | Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / PLA2 / Anti-inflammatory / Anti-coagulant / Indomethacin | ||||||
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 russellii (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Singh, N. / Prem Kumar, R. / Sharma, S. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: J.Mol.Recognit. / Year: 2009 Title: Simultaneous inhibition of anti-coagulation and inflammation: crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand-binding site Authors: Singh, N. / Kumar, R.P. / Kumar, S. / Sharma, S. / Mir, R. / 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 | 3h1x.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h1x.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3h1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1x ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1x | HTTPS FTP |
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-Related structure data
Related structure data | 1fb2S 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: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Strain: Viper Russells / References: UniProt: P59071, phospholipase A2 | ||
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#2: Chemical | ChemComp-IMN / | ||
#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: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.3M AMMONIUM SULPHATE, 30% PEG 4000 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2006 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→51.99 Å / Num. all: 24939 / Num. obs: 24939 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Rsym value: 0.045 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.418 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FB2 Resolution: 1.4→51.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.112 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.07 / 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: 21.888 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→51.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20 /
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