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- PDB-6ukw: STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ukw | ||||||
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Title | STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 10 | ||||||
![]() | fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain | ||||||
![]() | IMMUNE SYSTEM / AGONIST / STING (STIMULATOR OF INTERFERON GENES) / TRANSMEMBRANE PROTEIN 173 (TMEM173) / IMMUNE SYSTEM-INHIBITOR COMPLEX / IMMUNE SYSTEM-AGONIST COMPLEX | ||||||
Function / homology | ![]() SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / 2',3'-cyclic GMP-AMP binding / SUMOylation of SUMOylation proteins / cyclic-di-GMP binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / reticulophagy / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / autophagosome membrane / positive regulation of macroautophagy / protein sumoylation / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / condensed nuclear chromosome / PML body / protein tag activity / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lesburg, C.A. | ||||||
![]() | ![]() Title: An orally available non-nucleotide STING agonist with antitumor activity. Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / ...Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / Dandliker, P.J. / Feng, G. / Haidle, A. / Henderson, T. / Jewell, J. / Kariv, I. / Knemeyer, I. / Kopinja, J. / Lacey, B.M. / Laskey, J. / Lesburg, C.A. / Liang, R. / Long, B.J. / Lu, M. / Ma, Y. / Minnihan, E.C. / O'Donnell, G. / Otte, R. / Price, L. / Rakhilina, L. / Sauvagnat, B. / Sharma, S. / Tyagarajan, S. / Woo, H. / Wyss, D.F. / Xu, S. / Bennett, D.J. / Addona, G.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.7 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 356.3 KB | Display | ![]() |
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Full document | ![]() | 357.4 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ukmSC ![]() 6ukuC ![]() 6ukvC ![]() 6ukxC ![]() 6ukyC ![]() 6ukzC ![]() 6ul0C 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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Components
#1: Protein | Mass: 34456.527 Da / Num. of mol.: 2 / Mutation: G230A,R293Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c Gene: SMT3, YDR510W, D9719.15, STING, LOC340061, hCG_1782396 Plasmid: pET47b / Production host: ![]() ![]() #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: 1.71 Å3/Da / Density % sol: 28.02 % / Mosaicity: 0.06 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT |
-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: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→59.012 Å / Num. obs: 31056 / % possible obs: 95.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.077 / Rrim(I) all: 0.143 / Rsym value: 0.12 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.974→2.008 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 3.9 / Num. measured all: 13409 / Num. unique obs: 4160 / CC1/2: 0.644 / Rpim(I) all: 0.449 / Rrim(I) all: 0.841 / Rsym value: 0.834 / Net I/σ(I) obs: 4.1 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 6UKM Resolution: 1.97→25.39 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso max: 115.81 Å2 / Biso mean: 30.97 Å2 / Biso min: 8.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→25.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
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