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- PDB-8ahg: PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ahg | ||||||
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Title | PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery | ||||||
![]() | Serine/threonine-protein kinase PAK 4 | ||||||
![]() | TRANSFERASE / PROTEIN KINASE / PAK4 / ATP-BINDING / TECHNOLOGY | ||||||
Function / homology | ![]() dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOU GTPase cycle / cellular response to organic cyclic compound / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baker, L.M. / Murray, J.B. / Hubbard, R.E. | ||||||
Funding support | 1items
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![]() | ![]() Title: PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery. Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / ...Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / Harris, R. / Hendrickson, N. / Matassova, N. / Simmonite, H. / Smith, J. / Hubbard, R.E. / Liu, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 101.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.5 KB | Display | ![]() |
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Full document | ![]() | 787.2 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aheC ![]() 8ahfC ![]() 8ahhC ![]() 8ahiC ![]() 2bvaS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 33380.742 Da / Num. of mol.: 1 / Mutation: L310A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O96013, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-M4I / ~{ |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.94 % / Description: Prisms |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.8M Na/K tartrate 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 19, 2021 |
Radiation | Monochromator: Laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.885→58.496 Å / Num. obs: 27812 / % possible obs: 95.3 % / Redundancy: 26.4 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.018 / Rrim(I) all: 0.092 / Net I/av σ(I): 22.7 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.885→1.952 Å / Redundancy: 27.2 % / Rmerge(I) obs: 3.058 / Mean I/σ(I) obs: 1 / Num. unique obs: 1390 / CC1/2: 0.638 / Rpim(I) all: 0.588 / Rrim(I) all: 3.115 / % possible all: 50.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BVA Resolution: 1.885→58.496 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.598 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.137 Details: Hydrogens have been added in their riding positions
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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: 38.439 Å2
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Refinement step | Cycle: LAST / Resolution: 1.885→58.496 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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