[English] 日本語
Yorodumi- PDB-5s9m: AUTOTAXIN, (3,5-dichlorophenyl)methyl (3aS,8aR)-2-(1H-benzotriazo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5s9m | ||||||
---|---|---|---|---|---|---|---|
Title | AUTOTAXIN, (3,5-dichlorophenyl)methyl (3aS,8aR)-2-(1H-benzotriazole-5-carbonyl)-1,3,3a,4,5,7,8,8a-octahydropyrrolo[3,4-d]azepine-6-carboxylate, 1.80A, P212121, Rfree=21.1% | ||||||
Components | Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | ||||||
Keywords | HYDROLASE / LYSOPHOSPHATIDIC ACID / LPA / LYSOPHOSPHATIDYLCHOLINE / LPC / SOMATOMEDIN / METASTASIS / NEUROPATHIC PAIN / VASCULAR DEVELOPMENT / NEURAL DEVELOPMENT | ||||||
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: 1.8 Å | ||||||
Authors | Stihle, M. / Hunziker, D. / Benz, J. / Mattei, P. / Rudolph, M.G. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: To be published Title: Crystal Structure of a rat Autotaxin complex Authors: Hunziker, D. / Joachim, S.C. / Ullmer, C. / Rudolph, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5s9m.cif.gz | 200 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5s9m.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 5s9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/5s9m ftp://data.pdbj.org/pub/pdb/validation_reports/s9/5s9m | HTTPS FTP |
---|
-Group deposition
ID | G_1002194 (3 entries) |
---|---|
Type | undefined |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 97343.305 Da / Num. of mol.: 1 / Mutation: N53A, N410A, R591T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Plasmid: pcDNA3.1(-)_neo_rAtx(1-862_N53A:N410A) / Production host: Homo Sapiens (human) / Strain (production host): HEK 293-F References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase |
---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 8 types, 514 molecules
#3: Chemical | ChemComp-YV1 / ( | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.37 Å / Num. obs: 82778 / % possible obs: 99.9 % / Redundancy: 6.57 % / Biso Wilson estimate: 32.209 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.123 / Rsym value: 0.1 / Χ2: 0.843 / Net I/σ(I): 10.75 / Num. measured all: 553317 / Scaling rejects: 11 |
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 6.52 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.45 / Num. measured obs: 6146 / Num. possible: 1083 / Num. unique obs: 1074 / CC1/2: 0.999 / Rrim(I) all: 0.032 / Rsym value: 0.729 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model Resolution: 1.8→48.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.755 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 80 Å2 / Biso mean: 31.636 Å2 / Biso min: 14.03 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→48.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|