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Yorodumi- PDB-4zg6: Structural basis for inhibition of human autotaxin by four novel ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zg6 | |||||||||
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Title | Structural basis for inhibition of human autotaxin by four novel compounds | |||||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | |||||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Autotaxin / ENPP2 / inhibitor / Hydrolase-Hydrolase Inhibitor complex | |||||||||
Function / homology | Function and homology information Vitamin B5 (pantothenate) metabolism / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity ...Vitamin B5 (pantothenate) metabolism / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of epithelial cell migration / regulation of cell migration / cell motility / positive regulation of peptidyl-tyrosine phosphorylation / chemotaxis / nucleic acid binding / hydrolase activity / immune response / calcium ion binding / extracellular space / zinc ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | |||||||||
Model details | PAT-078 | |||||||||
Authors | Stein, A.J. / Bain, G. / Hutchinson, J.H. / Evans, J.F. | |||||||||
Citation | Journal: Mol.Pharmacol. / Year: 2015 Title: Structural Basis for Inhibition of Human Autotaxin by Four Potent Compounds with Distinct Modes of Binding. Authors: Stein, A.J. / Bain, G. / Prodanovich, P. / Santini, A.M. / Darlington, J. / Stelzer, N.M. / Sidhu, R.S. / Schaub, J. / Goulet, L. / Lonergan, D. / Calderon, I. / Evans, J.F. / Hutchinson, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zg6.cif.gz | 338.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zg6.ent.gz | 264.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zg6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4zg6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4zg6_validation.xml.gz | 61.5 KB | Display | |
Data in CIF | 4zg6_validation.cif.gz | 87.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/4zg6 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/4zg6 | HTTPS FTP |
-Related structure data
Related structure data | 4zg7C 4zg9C 4zgaC 3nkoS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 98332.578 Da / Num. of mol.: 2 / Fragment: UNP residues 17-863 / Mutation: N411A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP2, ATX, PDNP2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q13822, alkylglycerophosphoethanolamine phosphodiesterase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 640 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-NA / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-SCN / #9: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.4 M NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 10, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 154081 / % possible obs: 96.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.057 / Χ2: 1.554 / Net I/av σ(I): 18.981 / Net I/σ(I): 7.3 / Num. measured all: 303694 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2 % / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NKO Resolution: 1.8→34.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.905 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.642 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.69 Å
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