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- PDB-8r7e: MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8r7e | ||||||
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Title | MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mismatch bound form | ||||||
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![]() | DNA BINDING PROTEIN / PROTEROS BIOSTRUCTURES GMBH / DNA mismatch Repair | ||||||
Function / homology | ![]() somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity ...somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity / maintenance of DNA repeat elements / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mitotic recombination / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / oxidative phosphorylation / response to UV-B / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / ATP-dependent DNA damage sensor activity / germ cell development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / response to X-ray / somatic hypermutation of immunoglobulin genes / mismatch repair / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / male gonad development / double-strand break repair / double-stranded DNA binding / negative regulation of neuron apoptotic process / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. ...Thomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of orthosteric inhibitors of MutSbeta ATPase function Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. ...Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 772.7 KB | Display | ![]() |
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PDB format | ![]() | 585.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8r7cC C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-DNA mismatch repair protein ... , 2 types, 4 molecules AEBF
#1: Protein | Mass: 104431.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 104260.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 4 molecules CGDH
#3: DNA chain | Mass: 7345.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 6 types, 136 molecules 








#5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-CL / #8: Chemical | Mass: 487.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26FN7O2 / Feature type: SUBJECT OF INVESTIGATION #9: Chemical | ChemComp-SO4 / #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 MES pH 6.5; 0.2 M NH4 Acetate; 20-25 % 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 EIGER2 S 16M / Detector: PIXEL / Date: Aug 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.783→113.659 Å / Num. obs: 79309 / % possible obs: 92 % / Redundancy: 2.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.062 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.783→3.008 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3965 / CC1/2: 0.353 / Rpim(I) all: 0.643 / % possible all: 57.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.459 Å2
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Refinement step | Cycle: LAST / Resolution: 2.783→113.659 Å
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Refine LS restraints |
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