+Open data
-Basic information
Entry | Database: PDB / ID: 3unj | ||||||
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Title | CDK2 in complex with inhibitor YL1-038-31 | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / allosteric ligand / ANS / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9001 Å | ||||||
Authors | Zhu, J.-Y. / Martin, M.P. / Alam, R. / Schonbrunn, E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2012 Title: A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A. Authors: Martin, M.P. / Zhu, J.Y. / Lawrence, H.R. / Pireddu, R. / Luo, Y. / Alam, R. / Ozcan, S. / Sebti, S.M. / Lawrence, N.J. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3unj.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3unj.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3unj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3unj_validation.pdf.gz | 711 KB | Display | wwPDB validaton report |
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Full document | 3unj_full_validation.pdf.gz | 718.6 KB | Display | |
Data in XML | 3unj_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3unj_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/3unj ftp://data.pdbj.org/pub/pdb/validation_reports/un/3unj | HTTPS FTP |
-Related structure data
Related structure data | 3unkC 3unzC 3uo4C 3uo5C 3uo6C 3uodC 3uohC 3uojC 3uokC 3uolC 3up2C 3pxrS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-0BX / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5 mg/mL CDK2 protein, 1.5 mM YL1-038-31, 5 % (v/v) PEG 3350, 50 mM HEPES/NaOH (pH 7.5), 50 mM phosphate (Na/K, pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 12, 2009 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 22465 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7.5 / Rsym value: 0.254 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PXR Resolution: 1.9001→18.795 Å / SU ML: 0.25 / σ(F): 1.99 / Phase error: 25.18 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.945 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9001→18.795 Å
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Refine LS restraints |
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LS refinement shell |
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