[English] 日本語
Yorodumi- PDB-5kxa: Selective Inhibition of Autotaxin is Effective in Mouse Models of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kxa | ||||||
---|---|---|---|---|---|---|---|
Title | Selective Inhibition of Autotaxin is Effective in Mouse Models of Liver Fibrosis | ||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ENPP2 / autotaxin / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Vitamin B5 (pantothenate) metabolism / 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 ...Vitamin B5 (pantothenate) metabolism / 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 epithelial cell migration / regulation of cell migration / cell motility / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / 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 / Resolution: 2.59 Å | ||||||
Authors | Stein, A.J. / Bain, G. / Hutchinson, J.H. / Evans, J.F. | ||||||
Citation | Journal: J. Pharmacol. Exp. Ther. / Year: 2017 Title: Selective Inhibition of Autotaxin Is Efficacious in Mouse Models of Liver Fibrosis. Authors: Bain, G. / Shannon, K.E. / Huang, F. / Darlington, J. / Goulet, L. / Prodanovich, P. / Ma, G.L. / Santini, A.M. / Stein, A.J. / Lonergan, D. / King, C.D. / Calderon, I. / Lai, A. / Hutchinson, J.H. / Evans, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kxa.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kxa.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/5kxa ftp://data.pdbj.org/pub/pdb/validation_reports/kx/5kxa | HTTPS FTP |
---|
-Related structure data
Related structure data | 4zgaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 99042.578 Da / Num. of mol.: 1 / Mutation: N54A, 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: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 10 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-6Y7 / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.1 M Sodium Acetate pH 7 |
-Data collection
Diffraction | Mean temperature: 133 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Mar 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→65.84 Å / Num. obs: 23660 / % possible obs: 98.4 % / Redundancy: 1.1 % / Net I/σ(I): 7.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZGA Resolution: 2.59→65.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.562 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 53.771 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.59→65.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|