[English] 日本語
![](img/lk-miru.gif)
- PDB-6weu: Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-m... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6weu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate | ||||||
![]() | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / human E-NPP 1 / drug discovery / inhibitors / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / inorganic diphosphate transport / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism ...GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / inorganic diphosphate transport / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism / nucleotide diphosphatase / nucleoside triphosphate catabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / intracellular phosphate ion homeostasis / sequestering of triglyceride / nucleic acid metabolic process / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / phosphate ion homeostasis / negative regulation of bone mineralization / melanocyte differentiation / phosphodiesterase I activity / scavenger receptor activity / negative regulation of glucose import / regulation of bone mineralization / phosphate-containing compound metabolic process / exonuclease activity / polysaccharide binding / response to ATP / negative regulation of fat cell differentiation / bone mineralization / phosphatase activity / : / 3',5'-cyclic-AMP phosphodiesterase activity / ATP metabolic process / negative regulation of insulin receptor signaling pathway / generation of precursor metabolites and energy / insulin receptor binding / negative regulation of cell growth / cellular response to insulin stimulus / gene expression / basolateral plasma membrane / nucleic acid binding / immune response / lysosomal membrane / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / zinc ion binding / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. / Dennis, M. / Newman, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structures of human ENPP1 in apo and bound forms. Authors: Dennis, M.L. / Newman, J. / Dolezal, O. / Hattarki, M. / Surjadi, R.N. / Nuttall, S.D. / Pham, T. / Nebl, T. / Camerino, M. / Khoo, P.S. / Monahan, B.J. / Peat, T.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 356.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 56.1 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wetSC ![]() 6wevC ![]() 6wewC ![]() 6wfjC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AbABbB
#1: Protein | Mass: 105058.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P22413, phosphodiesterase I, nucleotide diphosphatase |
---|
-Sugars , 4 types, 9 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
---|---|---|---|---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 129 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SRA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SRA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / #7: Chemical | #8: Chemical | ChemComp-EDO / | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.9 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953731 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→47.613 Å / Num. obs: 82015 / % possible obs: 100 % / Redundancy: 26.9 % / CC1/2: 0.997 / Rpim(I) all: 0.055 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.65→2.7 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4439 / CC1/2: 0.508 / Rpim(I) all: 0.816 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 6WET Resolution: 2.65→47.57 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.139 / SU ML: 0.219 / Cross valid method: FREE R-VALUE / ESU R: 0.402 / ESU R Free: 0.265 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.145 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→47.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|