+Open data
-Basic information
Entry | Database: PDB / ID: 7p4k | ||||||
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Title | Soluble epoxide hydrolase in complex with FL217 | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE / Complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / phospholipid dephosphorylation / soluble epoxide hydrolase / lipid phosphatase activity / epoxide metabolic process / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / phospholipid dephosphorylation / soluble epoxide hydrolase / lipid phosphatase activity / epoxide metabolic process / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Ni, X. / Kramer, J.S. / Lillich, F. / Proschak, E. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Design of Dual Partial Peroxisome Proliferator-Activated Receptor gamma Agonists/Soluble Epoxide Hydrolase Inhibitors. Authors: Lillich, F.F. / Willems, S. / Ni, X. / Kilu, W. / Borkowsky, C. / Brodsky, M. / Kramer, J.S. / Brunst, S. / Hernandez-Olmos, V. / Heering, J. / Schierle, S. / Kestner, R.I. / Mayser, F.M. / ...Authors: Lillich, F.F. / Willems, S. / Ni, X. / Kilu, W. / Borkowsky, C. / Brodsky, M. / Kramer, J.S. / Brunst, S. / Hernandez-Olmos, V. / Heering, J. / Schierle, S. / Kestner, R.I. / Mayser, F.M. / Helmstadter, M. / Gobel, T. / Weizel, L. / Namgaladze, D. / Kaiser, A. / Steinhilber, D. / Pfeilschifter, W. / Kahnt, A.S. / Proschak, A. / Chaikuad, A. / Knapp, S. / Merk, D. / Proschak, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p4k.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p4k.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 7p4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p4k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7p4k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7p4k_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 7p4k_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p4k ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p4k | HTTPS FTP |
-Related structure data
Related structure data | 7p4eC 6fr2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 229 - 547 / Label seq-ID: 11 - 329
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-Components
#1: Protein | Mass: 39648.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.13 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→44.02 Å / Num. obs: 35542 / % possible obs: 92 % / Redundancy: 2.5 % / CC1/2: 0.996 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.15→2.22 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3151 / CC1/2: 0.835 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FR2 Resolution: 2.15→44.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.128 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.61 Å2 / Biso mean: 49.194 Å2 / Biso min: 27.83 Å2
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Refinement step | Cycle: final / Resolution: 2.15→44.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10084 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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