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Yorodumi- PDB-6dwd: SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dwd | ||||||
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Title | SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket | ||||||
Components | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | ||||||
Keywords | hydrolase/hydrolase inhibitor / Complex / deoxynucleoside triphosphate triphosphohydrolase / dNTPase / nucleotide analogue / Clofarabine-TP / HYDROLASE / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. ...Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl, J. / Keppler, O.T. / Xiong, Y. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1. Authors: Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl Jr., ...Authors: Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl Jr., J. / Keppler, O.T. / Xiong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dwd.cif.gz | 447 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dwd.ent.gz | 357.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/6dwd ftp://data.pdbj.org/pub/pdb/validation_reports/dw/6dwd | HTTPS FTP |
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-Related structure data
Related structure data | 6dw3C 6dw4C 6dw5C 6dw7C 6dwjC 6dwkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules DCBA
#1: Protein | Mass: 63426.375 Da / Num. of mol.: 4 / Mutation: H206R, D207N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases |
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-Non-polymers , 9 types, 1106 molecules
#2: Chemical | ChemComp-HDV / #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-GLY / #7: Chemical | #8: Chemical | ChemComp-PO4 / | #9: Chemical | ChemComp-TCE / | #10: 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: 2.03 Å3/Da / Density % sol: 39.54 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / Details: 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 209481 / % possible obs: 94.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4 % / Num. unique obs: 10532 / CC1/2: 0.283 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.687 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.104 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.521 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50 Å
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Refine LS restraints |
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