+Open data
-Basic information
Entry | Database: PDB / ID: 3rk9 | ||||||
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Title | CDK2 in complex with inhibitor RC-2-74 | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / 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: 1.85 Å | ||||||
Authors | Betzi, S. / Alam, R. / Han, H. / Becker, A. / Schonbrunn, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases. Authors: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / ...Authors: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / Hazlehurst, L.A. / Tash, J.S. / Georg, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rk9.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rk9.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rk9_validation.pdf.gz | 727.4 KB | Display | wwPDB validaton report |
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Full document | 3rk9_full_validation.pdf.gz | 736.7 KB | Display | |
Data in XML | 3rk9_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3rk9_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/3rk9 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/3rk9 | HTTPS FTP |
-Related structure data
Related structure data | 3qqkC 3qtqC 3qtrC 3qtsC 3qtuC 3qtwC 3qtxC 3qtzC 3qu0C 3qxpC 3r8uC 3r8vC 3r8zC 3r9dC 3r9hC 3r9nC 3r9oC 3rahC 3rakC 3ralC 3rjcC 3rk5C 3rk7C 3rkbC 3rmfC 3rniC 3rprC 3rpvC 3rpyC 3rzbC 3s00C 3s0oC 3s1hC 3sqqC 4gcjC 1pw2S 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: 34761.348 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-09Z / [ |
#3: 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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate, 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 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 25, 2008 / 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: 1.85→20 Å / Num. all: 24357 / Num. obs: 24357 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.93 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 6.82 / Num. unique all: 1816 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PW2 Resolution: 1.85→18.78 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1449023.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3894 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→18.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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