+Open data
-Basic information
Entry | Database: PDB / ID: 5l8l | ||||||
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Title | Aurora-A kinase domain in complex with vNAR-D01 (crystal form 1) | ||||||
Components |
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Keywords | TRANSFERASE / kinase / vNAR / inhibitor | ||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / T cell receptor complex / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / regulation of G2/M transition of mitotic cell cycle / SUMOylation of DNA replication proteins / spindle midzone / centriole / protein serine/threonine/tyrosine kinase activity / liver regeneration / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / response to wounding / spindle / peptide antigen binding / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / basolateral plasma membrane / midbody / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Orectolobus maculatus (spotted wobbegong) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Burgess, S.G. / Bayliss, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2016 Title: Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain. Authors: Burgess, S.G. / Oleksy, A. / Cavazza, T. / Richards, M.W. / Vernos, I. / Matthews, D. / Bayliss, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l8l.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l8l.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l8l_validation.pdf.gz | 825.4 KB | Display | wwPDB validaton report |
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Full document | 5l8l_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 5l8l_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 5l8l_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8l ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8l | HTTPS FTP |
-Related structure data
Related structure data | 5l8jC 5l8kC 2coqS 4cegS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32964.637 Da / Num. of mol.: 1 / Mutation: C290A, C393A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Plasmid: pET30TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 12766.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong) Plasmid: pET26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8JJ25 |
-Non-polymers , 4 types, 361 molecules
#3: Chemical | ChemComp-ADP / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 12.5 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→45.62 Å / Num. obs: 60106 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.67→1.71 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CEG, 2COQ Resolution: 1.67→44.435 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→44.435 Å
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Refine LS restraints |
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LS refinement shell |
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