+
Open data
-
Basic information
Entry | Database: PDB / ID: 6unq | ||||||
---|---|---|---|---|---|---|---|
Title | Kinase domain of ALK2-K493A with AMPPNP | ||||||
![]() | Activin receptor type-1 | ||||||
![]() | TRANSFERASE / Kinase | ||||||
Function / homology | ![]() endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / peptide hormone binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / in utero embryonic development / protein kinase activity / positive regulation of cell migration / cadherin binding / phosphorylation / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agnew, C. / Jura, N. | ||||||
![]() | ![]() Title: Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization. Authors: Agnew, C. / Ayaz, P. / Kashima, R. / Loving, H.S. / Ghatpande, P. / Kung, J.E. / Underbakke, E.S. / Shan, Y. / Shaw, D.E. / Hata, A. / Jura, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 765 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6unpC ![]() 6unrC ![]() 6unsC ![]() 3q4uS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38117.438 Da / Num. of mol.: 1 / Fragment: Kinase domain / Mutation: K493A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q04771, receptor protein serine/threonine kinase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ANP / | ||||
#3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES 6.5 pH, 20 %v/v Ethylene glycol, 7 %w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1111 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.07 Å / Num. obs: 14236 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 46.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.021 / Rrim(I) all: 0.034 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1478 / CC1/2: 0.987 / Rpim(I) all: 0.099 / Rrim(I) all: 0.159 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3Q4U Resolution: 2.4→49.07 Å / SU ML: 0.3355 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.659
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.07 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.4857138193 Å / Origin y: 18.9782625787 Å / Origin z: -17.5086773374 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |