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Yorodumi- PDB-5mql: Crystal structure of dCK mutant C3S in complex with masitinib and UDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mql | ||||||
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Title | Crystal structure of dCK mutant C3S in complex with masitinib and UDP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / Deoxycytidine kinase / dCK / masitinib | ||||||
Function / homology | Function and homology information deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Rebuffet, E. / Hammam, K. / Saez-Ayala, M. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. ...Rebuffet, E. / Hammam, K. / Saez-Ayala, M. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Pez, D. / Letard, S. / Mansfield, C. / Moussy, A. / de Sepulveda, P. / Morelli, X. / Dubreuil, P. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology. Authors: Hammam, K. / Saez-Ayala, M. / Rebuffet, E. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Letard, S. / Casteran, N. / ...Authors: Hammam, K. / Saez-Ayala, M. / Rebuffet, E. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Letard, S. / Casteran, N. / Mansfield, C. / Moussy, A. / De Sepulveda, P. / Morelli, X. / Dubreuil, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mql.cif.gz | 395.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mql.ent.gz | 324 KB | Display | PDB format |
PDBx/mmJSON format | 5mql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mql_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5mql_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5mql_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 5mql_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mql ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mql | HTTPS FTP |
-Related structure data
Related structure data | 5mqjC 5mqtC 1p60S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34023.195 Da / Num. of mol.: 4 / Mutation: C9S,C45S,C59S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Escherichia coli (E. coli) / References: UniProt: P27707, deoxycytidine kinase |
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-Non-polymers , 5 types, 26 molecules
#2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-G65 / | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium acetate, 20% PEG 3350, 50 mM NaCl, 24h soaking with 10 mM Masitinib |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885602 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885602 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→42.8 Å / Num. obs: 22378 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 138.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2677 / Net I/σ(I): 11.94 |
Reflection shell | Resolution: 3.25→3.366 Å / Redundancy: 8.6 % / Num. unique obs: 2164 / CC1/2: 0.832 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P60 Resolution: 3.25→47.8 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.519
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Displacement parameters | Biso mean: 97.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.25→47.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.41 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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