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- PDB-5uu1: Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) boun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uu1 | |||||||||
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Title | Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to BI-D1870 | |||||||||
![]() | Serine/threonine-protein kinase VRK2 | |||||||||
![]() | Transferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex | |||||||||
Function / homology | ![]() regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane ...regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane / nuclear envelope / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein kinase binding / signal transduction / endoplasmic reticulum / protein-containing complex / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Counago, R.M. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations. Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.1 KB | Display | ![]() |
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PDB format | ![]() | 107 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3op5C ![]() 5ukfC ![]() 5uvfC ![]() 2v62S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36788.230 Da / Num. of mol.: 1 / Fragment: UNP residues 14-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q86Y07, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-7DZ / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22.5% PEG 3350; 20 MM MAGNESIUM, CHLORIDE, 0.1M CHC BUFFER pH 7.5, STABILIZED WITH 20% (V/V) GLYCEROL PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45869 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.41 Å / Num. obs: 22504 / % possible obs: 98.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 35.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1633 / CC1/2: 0.891 / Rpim(I) all: 0.32 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V62 Resolution: 2→28.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.15
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Displacement parameters | Biso mean: 42.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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