+Open data
-Basic information
Entry | Database: PDB / ID: 7p4j | ||||||
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Title | Crystal structure of Autotaxin and tetrahydrocannabinol | ||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | ||||||
Keywords | HYDROLASE / Tetrahydrocannabinol / inhibitor | ||||||
Function / homology | Function and homology information response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell-matrix adhesion / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cellular response to cadmium ion / cell chemotaxis / cellular response to estradiol stimulus / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Eymery, M.C. / McCarthy, A.A. / Hausmann, J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Life Sci Alliance / Year: 2023 Title: Linking medicinal cannabis to autotaxin-lysophosphatidic acid signaling. Authors: Eymery, M.C. / McCarthy, A.A. / Hausmann, J. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p4j.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p4j.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 7p4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p4j ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p4j | HTTPS FTP |
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-Related structure data
Related structure data | 7p4oC 2xr9S 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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 95037.656 Da / Num. of mol.: 1 / Mutation: N410A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Production host: Homo sapiens (human) References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 10 types, 444 molecules
#3: Chemical | #4: Chemical | ChemComp-TCI / ( | #5: Chemical | ChemComp-5JK / | #6: Chemical | ChemComp-IOD / #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-PO4 / | #10: Chemical | #11: Chemical | ChemComp-NA / | #12: Water | ChemComp-HOH / | |
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-Details
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: 2.1 Å3/Da / Density % sol: 41.55 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 18-22% (m/v) PEG3350, 0.1-0.3 M NH4I and 0.3 M NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→61.24 Å / Num. obs: 47909 / % possible obs: 91.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 20.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.79→1.975 Å / Redundancy: 7 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 16845 / CC1/2: 0.49 / % possible all: 60.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XR9 Resolution: 1.79→61.24 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8006 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→61.24 Å
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Refine LS restraints |
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LS refinement shell |
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