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Yorodumi- PDB-1h0v: Human cyclin dependent protein kinase 2 in complex with the inhib... -
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-Basic information
Entry | Database: PDB / ID: 1h0v | ||||||
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Title | Human cyclin dependent protein kinase 2 in complex with the inhibitor 2-Amino-6-[(R)-pyrrolidino-5'-yl]methoxypurine | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / DRUG METABOLISM / MYCOBACTERIA / ISONIAZID / ARYLAMINE N-ACETYLTRANSFERASE / NAT / SERINE/THREONINE -PROTEIN KINASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / MITOSIS | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gibson, A.E. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Curtin, N.J. / Davies, T.G. / Endicott, J.A. / Golding, B.T. / Grant, S. / Griffin, R.J. ...Gibson, A.E. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Curtin, N.J. / Davies, T.G. / Endicott, J.A. / Golding, B.T. / Grant, S. / Griffin, R.J. / Jewsbury, P. / Johnson, L.N. / Mesguiche, V. / Newell, D.R. / Noble, M.E.M. / Tucker, J.A. / Whitfield, H.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Probing the ATP Ribose-Binding Domain of Cyclin-Dependent Kinases 1 and 2 with O(6)-Substituted Guanine Derivatives Authors: Gibson, A.E. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Curtin, N.J. / Davies, T.G. / Endicott, J.A. / Golding, B.T. / Grant, S. / Griffin, R.J. / Jewsbury, P. / Johnson, L.N. / Mesguiche, ...Authors: Gibson, A.E. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Curtin, N.J. / Davies, T.G. / Endicott, J.A. / Golding, B.T. / Grant, S. / Griffin, R.J. / Jewsbury, P. / Johnson, L.N. / Mesguiche, V. / Newell, D.R. / Noble, M.E.M. / Tucker, J.A. / Whitfield, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h0v.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h0v.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h0v_validation.pdf.gz | 332.4 KB | Display | wwPDB validaton report |
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Full document | 1h0v_full_validation.pdf.gz | 333.7 KB | Display | |
Data in XML | 1h0v_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1h0v_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h0v ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h0v | HTTPS FTP |
-Related structure data
Related structure data | 1gz8C 1h0wC 1e1vS 1h0u 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
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-UN4 / |
#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: 38.41 % |
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Crystal grow | Method: vapor diffusion / pH: 7.4 Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. ...Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. CDK2 CRYSTALS WERE SOAKED FOR 20 HOURS IN A SOLUTION OF 0.5MM NU2058 IN 1X WELL BUFFER PREPARED FROM STOCKS 2X WELLBUFFER AND 10MM NU2058 IN 100% DMSO. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 20657 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 1.4 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E1V Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.42 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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