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Open data
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Basic information
Entry | Database: PDB / ID: 8d0i | ||||||
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Title | Human SARM1 bound to an NB-3 eADPR adduct | ||||||
![]() | NAD(+) hydrolase SARM1 | ||||||
![]() | HYDROLASE/INHIBITOR / NAD / hydrolase / axon degeneration / neuroscience / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / nervous system process ...negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to axon injury / regulation of neuron apoptotic process / response to glucose / signaling adaptor activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / nervous system development / microtubule / mitochondrial outer membrane / cell differentiation / axon / innate immune response / synapse / dendrite / cell surface / signal transduction / protein-containing complex / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bratkowski, M.A. / Mathur, P. | ||||||
Funding support | 1items
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![]() | ![]() Title: Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease. Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / ...Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / Joseph, P.R.B. / Reynolds, C.H. / Sambashivan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 57.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d0cC ![]() 8d0dC ![]() 8d0eC ![]() 8d0fC ![]() 8d0gC ![]() 8d0hC ![]() 8d0jSC ![]() 8d0mC C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16205.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6SZW1, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 100 mM Bis-Tris propane pH 6.5, 200 mM potassium thiocyanate, and 15% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.4 Å / Num. obs: 20965 / % possible obs: 97.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.927 / Rmerge(I) obs: 0.524 / Rpim(I) all: 0.209 / Rrim(I) all: 0.565 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2066 / CC1/2: 0.826 / Rpim(I) all: 0.357 / Rrim(I) all: 0.957 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8D0J Resolution: 2→39.4 Å / SU ML: 0.201 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.946 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.4 Å
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Refine LS restraints |
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LS refinement shell |
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