+Open data
-Basic information
Entry | Database: PDB / ID: 7ukz | ||||||
---|---|---|---|---|---|---|---|
Title | CDK11 in complex with small molecule inhibitor OTS964 | ||||||
Components | Cyclin-dependent kinase 11B | ||||||
Keywords | TRANSFERASE/Inhibitor / Kinase / Inhibitor / TRANSFERASE / TRANSFERASE-Inhibitor complex | ||||||
Function / homology | Function and homology information regulation of mRNA processing / regulation of centrosome cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic cell cycle / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / mitotic cell cycle / regulation of apoptotic process / regulation of cell cycle ...regulation of mRNA processing / regulation of centrosome cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic cell cycle / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / mitotic cell cycle / regulation of apoptotic process / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / apoptotic process / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Kelso, S. / Sicheri, F. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Structure / Year: 2022 Title: Crystal structure of the CDK11 kinase domain bound to the small-molecule inhibitor OTS964. Authors: Kelso, S. / O'Brien, S. / Kurinov, I. / Angers, S. / Sicheri, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ukz.cif.gz | 347.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ukz.ent.gz | 276.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ukz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ukz_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ukz_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7ukz_validation.xml.gz | 63.7 KB | Display | |
Data in CIF | 7ukz_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/7ukz ftp://data.pdbj.org/pub/pdb/validation_reports/uk/7ukz | HTTPS FTP |
-Related structure data
Related structure data | 2iw8S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36590.480 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK11B, CDC2L1, CDK11, PITSLREA, PK58 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21127, cyclin-dependent kinase #2: Chemical | ChemComp-NK3 / #3: Chemical | ChemComp-SO4 / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.75M NH4SO4, 0.1M Tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.65 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→127.03 Å / Num. obs: 86275 / % possible obs: 99.9 % / Redundancy: 8.58 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.117 / Χ2: 0.823 / Net I/σ(I): 15.27 / Num. measured all: 740270 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IW8 homology model Resolution: 2.6→127.03 Å / Cross valid method: THROUGHOUT / σ(F): 248.55 / Phase error: 39.18 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.93 Å2 / Biso mean: 73.768 Å2 / Biso min: 42.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→127.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
|