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- PDB-6tx0: Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tx0 | |||||||||||||||
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Title | Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP and Mg | |||||||||||||||
![]() | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | |||||||||||||||
![]() | HYDROLASE / triphosphohydrolase / metallo-enzyme / binuclear / HD | |||||||||||||||
Function / homology | ![]() 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 / DNA strand resection involved in replication fork processing / deoxyribonucleotide 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 / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / 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 | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Morris, E.R. / Kunzelmann, S. / Caswell, S.J. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Authors: Morris, E.R. / Caswell, S.J. / Kunzelmann, S. / Arnold, L.H. / Purkiss, A.G. / Kelly, G. / Taylor, I.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 406 KB | Display | ![]() |
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PDB format | ![]() | 326.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.2 MB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6txaC ![]() 6txcC ![]() 6txeC ![]() 6txfC ![]() 6xu1C ![]() 6yomC ![]() 4bzcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 114 - 599 / Label seq-ID: 8 - 493
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60207.816 Da / Num. of mol.: 2 / Mutation: D137N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases |
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-Non-polymers , 5 types, 142 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/DZ4.gif)
![](data/chem/img/CZF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/DZ4.gif)
![](data/chem/img/CZF.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-DZ4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Bistris methane-HCl pH 6, 16% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.006→72.342 Å / Num. obs: 45483 / % possible obs: 95.6 % / Redundancy: 9.3 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Rrim(I) all: 0.12 / Net I/σ(I): 14.3 | ||||||||||||||||||||||||
Reflection shell | Num. unique obs: 2274 / Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4bzc Resolution: 2.01→72.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.397 / SU ML: 0.161 / SU R Cruickshank DPI: 0.3802 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.239 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 158.08 Å2 / Biso mean: 43.443 Å2 / Biso min: 17.45 Å2
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Refinement step | Cycle: final / Resolution: 2.01→72.31 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 30790 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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