+Open data
-Basic information
Entry | Database: PDB / ID: 3r7u | ||||||
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Title | CDK2 in complex with inhibitor KVR-1-75 | ||||||
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: 1.75 Å | ||||||
Authors | Betzi, S. / Alam, R. / Han, H. / Becker, A. / Schonbrunn, E. | ||||||
Citation | Journal: To be Published Title: Structure-guided optimization of novel CDK2 inhibitors discovered by high-throughput screening Authors: Schonbrunn, E. / Becker, A. / Betzi, S. / Alam, R. / Han, H. / Rawle, F. / Katta, V. / Jakkaraj, J. / Chakrasali, R. / Neelam, S. / Hook, D. / Tash, J. / Georg, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r7u.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r7u.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 3r7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r7u_validation.pdf.gz | 714.7 KB | Display | wwPDB validaton report |
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Full document | 3r7u_full_validation.pdf.gz | 722.7 KB | Display | |
Data in XML | 3r7u_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3r7u_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/3r7u ftp://data.pdbj.org/pub/pdb/validation_reports/r7/3r7u | HTTPS FTP |
-Related structure data
Related structure data | 3ql8C 3qqfC 3qqgC 3qqhC 3qqjC 3qqlC 3qrtC 3qruC 3qwjC 3qwkC 3qx2C 3qx4C 3qxoC 3qzfC 3qzgC 3qzhC 3qziC 3r1qC 3r1sC 3r1yC 3r28C 3r6xC 3r71C 3r73C 3r7eC 3r7iC 3r7vC 3r7yC 3r83C 3r8lC 3r8mC 3r8pC 3raiC 3rm6C 3rm7C 3royC 3rpoC 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-EDO / |
#3: Chemical | ChemComp-X96 / |
#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: 2.01 Å3/Da / Density % sol: 38.78 % |
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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: Aug 13, 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: 1.75→20 Å / Num. all: 28883 / Num. obs: 28883 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.95 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 12.68 / Num. unique all: 2312 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PW2 Resolution: 1.75→18.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1464499.45 / 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: 48.371 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→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: 1.75→1.86 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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