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- PDB-6c3l: Crystal structure of BCL6 BTB domain with compound 15f -

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Basic information

Entry
Database: PDB / ID: 6c3l
TitleCrystal structure of BCL6 BTB domain with compound 15f
ComponentsB-cell lymphoma 6 protein
Keywordsprotein binding/inhibitor / Inhibitor / protein-protein interaction / PROTEIN BINDING / protein binding-inhibitor complex
Function / homology
Function and homology information


regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / regulation of cell differentiation / negative regulation of cellular senescence / erythrocyte development / Rho protein signal transduction / regulation of immune response / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / protein localization / cell morphogenesis / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EGP / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46092157578 Å
AuthorsLinhares, B. / Cheng, H. / Cierpicki, T. / Xue, F.
CitationJournal: J.Med.Chem. / Year: 2018
Title: Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
Authors: Cheng, H. / Linhares, B.M. / Yu, W. / Cardenas, M.G. / Ai, Y. / Jiang, W. / Winkler, A. / Cohen, S. / Melnick, A. / MacKerell Jr., A. / Cierpicki, T. / Xue, F.
History
DepositionJan 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9804
Polymers29,8332
Non-polymers1,1482
Water5,152286
1
A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4902
Polymers14,9161
Non-polymers5741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4902
Polymers14,9161
Non-polymers5741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.930, 39.589, 55.182
Angle α, β, γ (deg.)83.754, 73.847, 66.962
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein B-cell lymphoma 6 protein / / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 14916.308 Da / Num. of mol.: 2 / Mutation: C10Q; C69R; C86N; E101V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Chemical ChemComp-EGP / N-[2-(1H-indol-3-yl)ethyl]-N'-{3-[(4-methylpiperazin-1-yl)methyl]-1-[2-(morpholin-4-yl)-2-oxoethyl]-1H-indol-6-yl}thiourea


Mass: 573.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H39N7O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5, 27% (w/v) PEG-3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 38467 / % possible obs: 95.9 % / Redundancy: 2 % / Biso Wilson estimate: 18.0435757244 Å2 / CC1/2: 0.066 / Net I/σ(I): 11.4
Reflection shellResolution: 1.46→1.51 Å / Num. unique all: 3801 / CC1/2: 0.316

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29
Resolution: 1.46092157578→30.0245580528 Å / SU ML: 0.149206247995 / Cross valid method: FREE R-VALUE / σ(F): 2.00336648389 / Phase error: 23.3608128619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235227182838 1873 4.86986817815 %
Rwork0.199753823845 36588 -
obs0.201385848596 38461 95.8386284917 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.6214781558 Å2
Refinement stepCycle: LAST / Resolution: 1.46092157578→30.0245580528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 82 286 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003027927535832102
X-RAY DIFFRACTIONf_angle_d0.5877145328522857
X-RAY DIFFRACTIONf_chiral_restr0.0639909086988333
X-RAY DIFFRACTIONf_plane_restr0.00261843725283352
X-RAY DIFFRACTIONf_dihedral_angle_d16.7499374138835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4609-1.50040.2701202069812090.2552298841392663X-RAY DIFFRACTION93.0654569021
1.5004-1.54460.2764802408681750.236835601562733X-RAY DIFFRACTION93.6855670103
1.5446-1.59440.236294277711300.2289714628482820X-RAY DIFFRACTION95.8103280286
1.5944-1.65140.2268469202311190.2119083885742823X-RAY DIFFRACTION94.9338496289
1.6514-1.71750.2554404515481110.2143897539412856X-RAY DIFFRACTION94.8529411765
1.7175-1.79570.2894708121681570.2138155266142793X-RAY DIFFRACTION96.5630114566
1.7957-1.89030.2521071224521240.2151360308972828X-RAY DIFFRACTION96.2818003914
1.8903-2.00870.2350818647141310.2023346435962806X-RAY DIFFRACTION96.4215364412
2.0087-2.16380.2729218852671570.2065702218982867X-RAY DIFFRACTION97.0474967908
2.1638-2.38150.231605936231630.1947968158552837X-RAY DIFFRACTION96.9305331179
2.3815-2.72590.2866709276991150.2011771363682884X-RAY DIFFRACTION98.1669394435
2.7259-3.43350.209445529671510.1929893790622872X-RAY DIFFRACTION96.9220904136
3.4335-30.03090.2041605416931310.1867535885842806X-RAY DIFFRACTION95.3571428571
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.04990277046-0.05138579806250.5462670151672.29044679552-0.9104480751783.53380079425-0.200194807642-0.1557871996690.06505283916220.3551821364040.1443491683010.0584401538583-0.448794449745-0.3293784809550.05717898192360.168611530630.0770828995990.01270377636330.16631182232-0.009028253303250.13884157914-30.17817362691.44797879561-1.58933718094
21.1711876147-0.128644733830.669495965362.057810650750.9108142275583.79716146413-0.2062469626840.1786216179920.0499526154615-0.3759820462570.147689319924-0.0428411466841-0.418359726550.3349918546560.07261523675030.187819601942-0.1013588818570.02367405557460.1790288624940.02445542248030.138500743254-18.9944338021.24157010833-21.9503666444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 5:128)
2X-RAY DIFFRACTION2(chain B and resseq 5:127)

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