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- PDB-5x9o: Crystal structure of the BCL6 BTB domain in complex with Compound 1a -

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Basic information

Entry
Database: PDB / ID: 5x9o
TitleCrystal structure of the BCL6 BTB domain in complex with Compound 1a
ComponentsB-cell lymphoma 6 protein
KeywordsTranscription/Inhibitor / Transcription Repressor / Transcription-Inhibitor complex
Function / homology
Function and homology information


negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain ...negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / regulation of immune response / regulation of cytokine production / transcription corepressor binding / 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 / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / zinc ion binding / identical protein 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-80R / : / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSogabe, S. / Ida, K. / Lane, W. / Snell, G.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design
Authors: Yasui, T. / Yamamoto, T. / Sakai, N. / Asano, K. / Takai, T. / Yoshitomi, Y. / Davis, M. / Takagi, T. / Sakamoto, K. / Sogabe, S. / Kamada, Y. / Lane, W. / Snell, G. / Iwata, M. / Goto, M. / ...Authors: Yasui, T. / Yamamoto, T. / Sakai, N. / Asano, K. / Takai, T. / Yoshitomi, Y. / Davis, M. / Takagi, T. / Sakamoto, K. / Sogabe, S. / Kamada, Y. / Lane, W. / Snell, G. / Iwata, M. / Goto, M. / Inooka, H. / Sakamoto, J.I. / Nakada, Y. / Imaeda, Y.
History
DepositionMar 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6944
Polymers16,2881
Non-polymers4063
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint2 kcal/mol
Surface area8950 Å2
2
A: B-cell lymphoma 6 protein
hetero molecules

A: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3878
Polymers32,5752
Non-polymers8126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4570 Å2
ΔGint-28 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.618, 66.618, 151.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-913-

HOH

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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: 16287.733 Da / Num. of mol.: 1 / Fragment: UNP residues 5-129
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-80R / 5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one


Mass: 304.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClN4O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris, potassium/sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 27912 / % possible obs: 98.8 % / Redundancy: 9.2 % / Rsym value: 0.063 / Net I/σ(I): 26.8
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.78 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 1.58→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.203 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21329 1390 5 %RANDOM
Rwork0.19929 ---
obs0.20001 26383 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.58→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 26 95 1163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191125
X-RAY DIFFRACTIONr_bond_other_d0.0020.021048
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9881533
X-RAY DIFFRACTIONr_angle_other_deg0.98732427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8875145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47223.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.758159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02250
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1262.062538
X-RAY DIFFRACTIONr_mcbond_other1.1262.055537
X-RAY DIFFRACTIONr_mcangle_it1.973.081676
X-RAY DIFFRACTIONr_mcangle_other1.9693.09677
X-RAY DIFFRACTIONr_scbond_it1.5482.486587
X-RAY DIFFRACTIONr_scbond_other1.5452.486587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5573.635851
X-RAY DIFFRACTIONr_long_range_B_refined5.09826.1621302
X-RAY DIFFRACTIONr_long_range_B_other4.94425.7161285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 89 -
Rwork0.291 1843 -
obs--95.83 %
Refinement TLS params.Method: refined / Origin x: -30.6022 Å / Origin y: 23.9925 Å / Origin z: -3.3714 Å
111213212223313233
T0.0168 Å2-0.0015 Å2-0.0097 Å2-0.053 Å2-0.045 Å2--0.0461 Å2
L0.5361 °20.0147 °20.289 °2-0.1756 °20.3862 °2--0.9951 °2
S0.0114 Å °-0.0744 Å °0.0482 Å °-0.0147 Å °-0.0054 Å °0.0018 Å °-0.0164 Å °-0.0147 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 129
2X-RAY DIFFRACTION1A801

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