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- PDB-5x4p: Crystal structure of the BCL6 BTB domain in complex with Compound 6 -

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Basic information

Entry
Database: PDB / ID: 5x4p
TitleCrystal structure of the BCL6 BTB domain in complex with Compound 6
ComponentsB-cell lymphoma 6 protein
KeywordsTranscription/Inhibitor / Transcription Repressor / Transcription-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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...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 plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of cell motility / negative regulation of B cell apoptotic process / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of T cell proliferation / B cell proliferation / negative regulation of cellular senescence / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / regulation of immune response / Rho protein signal transduction / positive regulation of B cell proliferation / positive regulation of neuron differentiation / regulation of cytokine production / cell-matrix adhesion / transcription corepressor binding / cell motility / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell morphogenesis / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / 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 / DNA damage response / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / zinc ion binding / nucleoplasm / 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-7ZO / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSogabe, S. / Ida, K. / Lane, W. / Snell, G.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach
Authors: Kamada, Y. / Sakai, N. / Sogabe, S. / Ida, K. / Oki, H. / Sakamoto, K. / Lane, W. / Snell, G. / Iida, M. / Imaeda, Y. / Sakamoto, J. / Matsui, J.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
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_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,5482
Polymers16,2881
Non-polymers2611
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8950 Å2
Unit cell
Length a, b, c (Å)66.728, 66.728, 155.325
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-903-

HOH

21A-916-

HOH

31A-922-

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-7ZO / 5-[(5-chloranylpyrimidin-4-yl)amino]-1,3-dihydroindol-2-one


Mass: 260.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
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: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 13032 / % possible obs: 97.5 % / Redundancy: 11.5 % / Rsym value: 0.069 / Net I/σ(I): 28.5
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.3 / Rsym value: 1 / % possible all: 86

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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: 2.06→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.735 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21941 639 4.9 %RANDOM
Rwork0.19313 ---
obs0.19444 12329 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.06→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 18 25 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191078
X-RAY DIFFRACTIONr_bond_other_d0.0010.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9821456
X-RAY DIFFRACTIONr_angle_other_deg0.99432329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48423.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82815194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.472159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
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_it1.7994.007519
X-RAY DIFFRACTIONr_mcbond_other1.7994.001518
X-RAY DIFFRACTIONr_mcangle_it2.8255.992647
X-RAY DIFFRACTIONr_mcangle_other2.8236648
X-RAY DIFFRACTIONr_scbond_it2.2884.351559
X-RAY DIFFRACTIONr_scbond_other2.2864.35560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7146.399810
X-RAY DIFFRACTIONr_long_range_B_refined5.29746.6851189
X-RAY DIFFRACTIONr_long_range_B_other5.2946.6191188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.063→2.116 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 59 -
Rwork0.272 773 -
obs--88.32 %
Refinement TLS params.Method: refined / Origin x: 31.128 Å / Origin y: -24.1127 Å / Origin z: -3.529 Å
111213212223313233
T0.0206 Å2-0.0234 Å2-0.0124 Å2-0.1514 Å20.103 Å2--0.0809 Å2
L3.059 °20.6613 °2-1.3104 °2-2.0151 °2-1.5866 °2--3.4035 °2
S0.1801 Å °-0.4992 Å °-0.256 Å °0.0571 Å °-0.0682 Å °-0.0411 Å °-0.0029 Å °0.0347 Å °-0.1119 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 129
2X-RAY DIFFRACTION1A801

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