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- PDB-7afw: Beta-Catenin in complex with compound 6 -

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Basic information

Entry
Database: PDB / ID: 7afw
TitleBeta-Catenin in complex with compound 6
ComponentsCatenin beta-1
KeywordsONCOPROTEIN / Fragment
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / adherens junction assembly / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / Formation of axial mesoderm / lung-associated mesenchyme development / negative regulation of protein sumoylation / embryonic heart tube development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Chem-R9Q / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.814 Å
AuthorsBoettcher, J. / Kessler, D.
CitationJournal: Chemmedchem / Year: 2021
Title: Getting a Grip on the Undrugged: Targeting beta-Catenin with Fragment-Based Methods.
Authors: Kessler, D. / Mayer, M. / Zahn, S.K. / Zeeb, M. / Wohrle, S. / Bergner, A. / Bruchhaus, J. / Ciftci, T. / Dahmann, G. / Dettling, M. / Dobel, S. / Fuchs, J.E. / Geist, L. / Hela, W. / ...Authors: Kessler, D. / Mayer, M. / Zahn, S.K. / Zeeb, M. / Wohrle, S. / Bergner, A. / Bruchhaus, J. / Ciftci, T. / Dahmann, G. / Dettling, M. / Dobel, S. / Fuchs, J.E. / Geist, L. / Hela, W. / Kofink, C. / Kousek, R. / Moser, F. / Puchner, T. / Rumpel, K. / Scharnweber, M. / Werni, P. / Wolkerstorfer, B. / Breitsprecher, D. / Baaske, P. / Pearson, M. / McConnell, D.B. / Bottcher, J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4542
Polymers18,1761
Non-polymers2781
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.453, 53.453, 87.545
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

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Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 18176.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / References: UniProt: P35222
#2: Chemical ChemComp-R9Q / 3-[(2~{R})-4-methyl-5-oxidanylidene-2,3-dihydro-1,4-benzoxazepin-2-yl]benzenecarbonitrile


Mass: 278.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: 25% PEG 3350, 100 mM BIS-TRIS buffer pH 5.5 and 0.2 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.814→87.545 Å / Num. obs: 11045 / % possible obs: 80.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 24.6
Reflection shellResolution: 1.814→1.929 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1 / Num. unique obs: 1066 / Rsym value: 0.825 / % possible all: 24.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XDSJan 26, 201data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SLA

3sla


Resolution: 1.814→87.55 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.811 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 551 -RANDOM
Rwork0.2272 ---
obs0.2299 11045 80.8 %-
Displacement parametersBiso mean: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.3237 Å20 Å20 Å2
2--2.3237 Å20 Å2
3----4.6475 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 1.814→87.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 21 69 1314
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091261HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.971706HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d456SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes211HARMONIC5
X-RAY DIFFRACTIONt_it1261HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion174SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1133SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion17.42
LS refinement shellResolution: 1.814→1.91 Å
RfactorNum. reflection% reflection
Rfree0.3613 24 -
Rwork0.2498 --
obs--21.05 %
Refinement TLS params.Origin x: 70.298 Å / Origin y: -30.7596 Å / Origin z: 22.2517 Å
111213212223313233
T-0.0392 Å20.0073 Å20.0392 Å2-0.03 Å20.0358 Å2---0.0939 Å2
L0.7963 °20.3018 °20.4623 °2-0.7771 °20.3635 °2--2.6755 °2
S-0.0628 Å °-0.0536 Å °-0.0236 Å °-0.0536 Å °-0.0037 Å °0.3457 Å °-0.0236 Å °0.3457 Å °0.0665 Å °
Refinement TLS groupSelection details: { A|* }

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