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- PDB-5n20: Crystal structure of the BCL6 BTB domain in complex with pyrazolo... -

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Basic information

Entry
Database: PDB / ID: 5n20
TitleCrystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine ligand
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSFERASE / KINASE
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-8GN / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsRobb, G. / Ferguson, A. / Hargreaves, D.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors.
Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / ...Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / Fillery, S. / Fuller, N.O. / Gangl, E. / Gao, N. / Grist, M. / Hargreaves, D. / Howard, M.R. / Hu, J. / Kemmitt, P.D. / Nelson, J.E. / O'Connell, N. / Prince, D.B. / Raubo, P. / Rawlins, P.B. / Robb, G.R. / Shi, J. / Waring, M.J. / Whittaker, D. / Wylot, M. / Zhu, X.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6752
Polymers14,2161
Non-polymers4601
Water1,24369
1
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3504
Polymers28,4312
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4010 Å2
ΔGint-27 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.520, 71.660, 54.660
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number5
Space group name H-MC121

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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: 14215.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Komagataella pastoris (fungus) / References: UniProt: P41182
#2: Chemical ChemComp-8GN / ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-[(3~{R})-3-(dimethylamino)pyrrolidin-1-yl]phenyl]ethanamide


Mass: 459.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N9O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→35.83 Å / Num. obs: 22955 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.77 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 13.7
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.3 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→15.25 Å / Cor.coef. Fo:Fc: 0.9493 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1172 5.14 %RANDOM
Rwork0.199 ---
obs0.2002 22815 97.89 %-
Displacement parametersBiso mean: 31.45 Å2
Baniso -1Baniso -2Baniso -3
1--5.3528 Å20 Å20.0371 Å2
2--2.3976 Å20 Å2
3---2.9552 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.38→15.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 34 69 1112
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011066HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.061450HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d403SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes186HARMONIC5
X-RAY DIFFRACTIONt_it1066HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion13.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion141SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1345SEMIHARMONIC4
LS refinement shellResolution: 1.38→1.45 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.286 140 4.78 %
Rwork0.2362 2790 -
all0.2387 2930 -
obs--97.89 %
Refinement TLS params.Method: refined / Origin x: 2.8284 Å / Origin y: -1.5491 Å / Origin z: 16.0448 Å
111213212223313233
T0.1188 Å2-0.0761 Å2-0.0001 Å2--0.0813 Å2-0.0129 Å2---0.0837 Å2
L0.4149 °20.0894 °2-0.2853 °2-0.9351 °2-0.7088 °2--2.592 °2
S-0.1677 Å °0.0941 Å °-0.0239 Å °-0.2654 Å °0.1012 Å °0.0057 Å °0.5384 Å °-0.208 Å °0.0665 Å °
Refinement TLS groupSelection details: { A|* }

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