+Open data
-Basic information
Entry | Database: PDB / ID: 6wqx | ||||||
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Title | Human PRPK-TPRKB complex | ||||||
Components |
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Keywords | PROTEIN BINDING/TRANSFERASE / tRNA modification / kinase / protein binding / PROTEIN BINDING-TRANSFERASE complex | ||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / hydrolase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Li, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G. | ||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Crystal structure of the human PRPK-TPRKB complex. Authors: Li, J. / Ma, X. / Banerjee, S. / Chen, H. / Ma, W. / Bode, A.M. / Dong, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wqx.cif.gz | 386.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wqx.ent.gz | 258.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/6wqx ftp://data.pdbj.org/pub/pdb/validation_reports/wq/6wqx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20130.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPRKB, CGI-121, My019 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C4 #2: Protein | Mass: 29755.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53RK, C20orf64, PRPK / Production host: Escherichia coli (E. coli) References: UniProt: Q96S44, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M KCl, 0.1 M HEPES pH 7.5, 15% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→49.36 Å / Num. obs: 32683 / % possible obs: 99.1 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.53→2.64 Å / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2 / Num. unique obs: 3987 / CC1/2: 0.806 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ENP, 3EN9 Resolution: 2.53→49.358 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.53→49.358 Å
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Refine LS restraints |
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LS refinement shell |
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